1
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Duncan KM, Trousdale RC, Gonzales CN, Steel WH, Walker RA. l-Phenylalanine Partitioning Mechanisms in Model Biological Membranes. J Phys Chem B 2023. [PMID: 37315336 DOI: 10.1021/acs.jpcb.2c08582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Time-resolved fluorescence spectroscopy in combination with differential scanning calorimetry (DSC) was used to study the chemical interactions that occur when l-phenylalanine is introduced to solutions containing phosphatidylcholine vesicles. Studies reported in this work address open questions about l-Phe's affinity for lipid vesicle bilayers, the effects of l-Phe partitioning on bilayer properties, l-Phe's solvation within a lipid bilayer, and the amount of l-Phe within that local solvation environment. DSC data show that l-Phe reduces the amount of heat necessary to melt saturated phosphatidylcholine bilayers from their gel to liquid-crystalline state but does not change the transition temperature (Tgel-lc). Time-resolved emission shows only a single l-Phe lifetime at low temperatures corresponding to l-Phe remaining solvated in aqueous solution. At temperatures close to Tgel-lc, a second, shorter lifetime appears that is assigned to l-Phe already embedded within the membrane that becomes hydrated as water starts to permeate the lipid bilayer. This new lifetime is attributed to a conformationally restricted rotamer in the bilayer's polar headgroup region and accounts for up to 30% of the emission amplitude. Results reported for dipalmitoylphosphatidylcholine (DPPC, 16:0) lipid vesicles prove to be general, with similar effects observed for dimyristoylphosphatidylcholine (DMPC, 14:0) and distearoylphosphatidylcholine (DSPC, 18:0) vesicles. Taken together, these results create a complete and compelling picture of how l-Phe associates with model biological membranes. Furthermore, this approach to examining amino acid partitioning into membranes and the resulting solvation forces points to new strategies for studying the structure and chemistry of membrane-soluble peptides and selected membrane proteins.
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Affiliation(s)
- Katelyn M Duncan
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Rhys C Trousdale
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Cristina N Gonzales
- Department of Chemistry, Reed College, Portland, Oregon 97202, United States
| | - William H Steel
- Department of Chemistry, York College of Pennsylvania, York, Pennsylvania 17403, United States
| | - Robert A Walker
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
- Montana Materials Science Program, Montana State University, Bozeman, Montana 59717, United States
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2
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Rawson KM, Lacey MM, Strong PN, Miller K. Improving the Therapeutic Index of Smp24, a Venom-Derived Antimicrobial Peptide: Increased Activity against Gram-Negative Bacteria. Int J Mol Sci 2022; 23:ijms23147979. [PMID: 35887325 PMCID: PMC9320964 DOI: 10.3390/ijms23147979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/13/2022] [Accepted: 07/18/2022] [Indexed: 11/16/2022] Open
Abstract
Antimicrobial peptides (AMPs) are naturally occurring compounds which possess a rapid killing mechanism and low resistance potential. Consequently, they are being viewed as potential alternatives to traditional antibiotics. One of the major factors limiting further development of AMPs is off-target toxicity. Enhancements to antimicrobial peptides which can maximise antimicrobial activity whilst reducing mammalian cytotoxicity would make these peptides more attractive as future pharmaceuticals. We have previously characterised Smp24, an AMP derived from the venom of the scorpion Scorpio maurus palmatus. This study sought to better understand the relationship between the structure, function and bacterial selectivity of this peptide by performing single amino acid substitutions. The antimicrobial, haemolytic and cytotoxic activity of modified Smp24 peptides was determined. The results of these investigations were compared with the activity of native Smp24 to determine which modifications produced enhanced therapeutic indices. The structure–function relationship of Smp24 was investigated by performing N-terminal, mid-chain and C-terminal amino acid substitutions and determining the effect that they had on the antimicrobial and cytotoxic activity of the peptide. Increased charge at the N-, mid- and C-termini of the peptide resulted in increased antimicrobial activity. Increased hydrophobicity at the N-terminus resulted in reduced haemolysis and cytotoxicity. Reduced antimicrobial, haemolytic and cytotoxic activity was observed by increased hydrophobicity at the mid-chain. Functional improvements have been made to modified peptides when compared with native Smp24, which has produced peptides with enhanced therapeutic indices.
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3
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Assies L, Mercier V, López-Andarias J, Roux A, Sakai N, Matile S. The Dynamic Range of Acidity: Tracking Rules for the Unidirectional Penetration of Cellular Compartments. Chembiochem 2022; 23:e202200192. [PMID: 35535626 PMCID: PMC9400975 DOI: 10.1002/cbic.202200192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/09/2022] [Indexed: 12/03/2022]
Abstract
Labeled ammonium cations with pKa∼7.4 accumulate in acidic organelles because they can be neutralized transiently to cross the membrane at cytosolic pH 7.2 but not at their internal pH<5.5. Retention in early endosomes with less acidic internal pH was achieved recently using weaker acids of up to pKa 9.8. We report here that primary ammonium cations with higher pKa 10.6, label early endosomes more efficiently. This maximized early endosome tracking coincides with increasing labeling of Golgi networks with similarly weak internal acidity. Guanidinium cations with pKa 13.5 cannot cross the plasma membrane in monomeric form and label the plasma membrane with selectivity for vesicles embarking into endocytosis. Self‐assembled into micelles, guanidinium cations enter cells like arginine‐rich cell‐penetrating peptides and, driven by their membrane potential, penetrate mitochondria unidirectionally despite their high inner pH. The resulting tracking rules with an approximated dynamic range of pKa change ∼3.5 are expected to be generally valid, thus enabling the design of chemistry tools for biology research in the broadest sense. From a practical point of view, most relevant are two complementary fluorescent flipper probes that can be used to image the mechanics at the very beginning of endocytosis.
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Affiliation(s)
- Lea Assies
- University of Geneva Faculty of Science: Universite de Geneve Faculte des Sciences, School of Chemistry and Biochemistry, SWITZERLAND
| | - Vincent Mercier
- University of Geneva Faculty of Science: Universite de Geneve Faculte des Sciences, School of Chemistry and Biochemistry, SWITZERLAND
| | - Javier López-Andarias
- University of Geneva Faculty of Science: Universite de Geneve Faculte des Sciences, School of Chemistry and Biochemistry, SWITZERLAND
| | - Aurelien Roux
- University of Geneva Faculty of Science: Universite de Geneve Faculte des Sciences, School of Chemistry and Biochemistry, SWITZERLAND
| | - Naomi Sakai
- University of Geneva Faculty of Science: Universite de Geneve Faculte des Sciences, School of Chemistry and Biochemistry, SWITZERLAND
| | - Stefan Matile
- University of Geneva, Department of Organic Chemistry, Quai Ernest-Ansermet 30, CH-1211, Geneva, SWITZERLAND
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4
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Riedlová K, Dolejšová T, Fišer R, Cwiklik L. H1 helix of colicin U causes phospholipid membrane permeation. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183866. [PMID: 35007517 DOI: 10.1016/j.bbamem.2022.183866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 12/29/2021] [Accepted: 01/03/2022] [Indexed: 06/14/2023]
Abstract
In light of an increasing number of antibiotic-resistant bacterial strains, it is essential to understand an action imposed by various antimicrobial agents on bacteria at the molecular level. One of the leading mechanisms of killing bacteria is related to the alteration of their plasmatic membrane. We study bio-inspired peptides originating from natural antimicrobial proteins colicins, which can disrupt membranes of bacterial cells. Namely, we focus on the α-helix H1 of colicin U, produced by bacterium Shigella boydii, and compare it with analogous peptides derived from two different colicins. To address the behavior of the peptides in biological membranes, we employ a combination of molecular simulations and experiments. We use molecular dynamics simulations to show that all three peptides are stable in model zwitterionic and negatively charged phospholipid membranes. At the molecular level, their embedment leads to the formation of membrane defects, membrane permeation for water, and, for negatively charged lipids, membrane poration. These effects are caused by the presence of polar moieties in the considered peptides. Importantly, simulations demonstrate that even monomeric H1 peptides can form toroidal pores. At the macroscopic level, we employ experimental co-sedimentation and fluorescence leakage assays. We show that the H1 peptide of colicin U incorporates into phospholipid vesicles and disrupts their membranes, causing leakage, in agreement with the molecular simulations. These insights obtained for model systems seem important for understanding the mechanisms of antimicrobial action of natural bacteriocins and for future exploration of small bio-inspired peptides able to disrupt bacterial membranes.
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Affiliation(s)
- Kamila Riedlová
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223 Prague, Czech Republic; Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Hlavova 8, 12800 Prague, Czech Republic
| | - Tereza Dolejšová
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223 Prague, Czech Republic; Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 12843 Prague, Czech Republic
| | - Radovan Fišer
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 12843 Prague, Czech Republic.
| | - Lukasz Cwiklik
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223 Prague, Czech Republic.
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5
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Zhang B, Peng Y, Wang Y, Wang X. Exploring the trimerization process of a transmembrane helix with an ionizable residue by molecular dynamics simulations: a case study of transmembrane domain 5 of LMP-1. Phys Chem Chem Phys 2022; 24:7084-7092. [PMID: 35262149 DOI: 10.1039/d2cp00102k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The oligomerization of membrane proteins is an important biological process that plays a critical role in the initialization of membrane protein receptor signaling. Unveiling how transmembrane segments oligomerize is critical for understanding the mechanism of membrane receptor signaling activation. Owing to the complicated membrane environment and the extraordinary dynamic properties of the ionizable residues in the transmembrane segment, it is extremely challenging to thoroughly understand the oligomerization process of the transmembrane domain. In this study, transmembrane domain 5 (TMD5) of latent membrane protein-1 from Epstein-Barr virus was used as a prototype model to investigate the trimerization process of the transmembrane segment with ionizable residues. The trimerization process of TMD5 was rebuilt and investigated via conventional molecular dynamics simulations and constant-pH molecular dynamics simulations. When TMD5s approached each other, the tilting angles of the TMD5 monomer decreased. TMD5s formed stable trimers until two interacting sites (D150s and Q139s) along each transmembrane helix were created to lock the TMD5s. The pKa values of D150 shifted toward neutral states in the membrane environment. When TMD5s were monomers, the pKa shift of D150 was mainly influenced by its microenvironment in the lipid bilayer. When TMD5s were moving close to each other, protein-protein interactions became the main contributing factor for the pKa shift of D150s. Overall, this work elucidates the behavior of the TMD5 helix and the pKa shift of ionizable residue D150 in the process of TMD5 oligomerization. This study may provide insight into the development of agents for targeting the oligomerization of membrane proteins.
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Affiliation(s)
- Bo Zhang
- Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China. .,Department of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Yinghua Peng
- State Key Laboratory for Molecular Biology of Special Economic Animal, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, Jilin, 130112, China
| | - Yibo Wang
- Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China.
| | - Xiaohui Wang
- Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China. .,Department of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, Anhui, 230026, China.,Beijing National Laboratory for Molecular Sciences, Beijing, 100190, China
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6
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Johnson JL, Huang J, Rooney M, Gu C. Optimal pH 8.5 to 9 for the Hydrolysis of Vixotrigine and Other Basic Substrates of Carboxylesterase-1 in Human Liver Microsomes. Xenobiotica 2021; 52:105-112. [PMID: 34904522 DOI: 10.1080/00498254.2021.2018629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Vixotrigine is a voltage- and use-dependent sodium channel blocker under investigation for the potential treatment of neuropathic pain. One of the major in vivo metabolic pathways of vixotrigine in humans is the hydrolysis of the carboxamide to form the carboxylic acid metabolite M14.The in vitro formation of M14 in human hepatocytes was inhibited by the carboxylesterase (CES) inhibitor Bis(4-nitrophenyl) phosphate in a concentration-dependent manner. The hydrolysis reaction was identified to be catalyzed by recombinant human CES1b.Initial observation of only trace level formation of M14 in human liver microsomes at pH 7.4 caused us to doubt the involvement of CES1, an enzyme localized at the endoplasmic reticulum and the dominant carboxylesterase in human liver. Further investigation has revealed that optimal pH for the hydrolysis of vixotrigine and two other basic substrates of CES1, methylphenidate and oseltamivir, in human liver microsomes was pH 8.5 to 9 which is higher than their respective pKa(base), suggesting that neutral form of basic substrates is probably preferred for CES1 catalysis in liver microsomes.
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Affiliation(s)
- Joshua L Johnson
- Drug Metabolism and Pharmacokinetics.,Current affiliation of JLJ: Drug Metabolism and Pharmacokinetics, Takeda, San Diego, CA, USA
| | | | - Michael Rooney
- Clinical Pharmacology and Pharmacometrics, Biogen, Cambridge, MA, USA
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7
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BTK-inhibitor drug covalent binding to lysine in human serum albumin using LC-MS/MS. Drug Metab Pharmacokinet 2021; 42:100433. [PMID: 34896750 DOI: 10.1016/j.dmpk.2021.100433] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 10/29/2021] [Accepted: 11/04/2021] [Indexed: 11/23/2022]
Abstract
Irreversible Bruton's tyrosine kinase (BTK) inhibitor drugs are designed to bind covalently to a free-thiol cysteine in the BTK protein active site. However, these reactive drugs bind to off-target proteins as well. In this study, seven BTK-inhibitor drugs containing acrylamide warheads were incubated with human serum albumin (HSA) and analyzed using an LC-MS/MS peptide mapping approach to determine the amino acid sites of drug covalent binding. Significant adduction at the free-thiol cysteine of HSA was only observed for two of the drugs. However, significant adduction was observed for at least four lysine residues. This is just a small percentage of the 59 total lysine residues in HSA. These four lysine residues are likely partially buried, accessible to the drugs, and exist at least partially in a neutral state. The levels of adduction observed in the in-vitro experimental conditions are only indicative of a relative propensity for adduction with the individual lysine residues of HSA, and are not in-vivo predictions. Widespread off-target lysine binding could impact clearance and bioavailability for irreversible inhibitor drugs. However, the extent of the impact on clearance may be limited in comparison to conjugation with glutathione.
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8
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Price JR, Afrose F, Greathouse DV, Koeppe RE. Illuminating Disorder Induced by Glu in a Stable Arg-Anchored Transmembrane Helix. ACS OMEGA 2021; 6:20611-20618. [PMID: 34396006 PMCID: PMC8359125 DOI: 10.1021/acsomega.1c02800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 07/13/2021] [Indexed: 06/13/2023]
Abstract
Membrane proteins are vital for biological function and are complex to study. Even in model peptide-lipid systems, the combined influence or interaction of pairs of chemical groups still is not well understood. Disordered proteins, whether in solution or near lipid membranes, are an emerging paradigm for the initiation and control of biological function. The disorder can involve molecular orientation as well as molecular folding. This paper reports an astonishing induction of disorder when one Glu residue is introduced into a highly stable 23-residue transmembrane helix. The parent helix is anchored by a single Arg residue, tilted at a well-defined angle with respect to the DOPC bilayer normal and undergoes rapid cone precession. When Glu is introduced two residues away from Arg, with 200° (or 160°) radial separation, the helix properties change radically to exhibit a multiplicity of three or more disordered states. The helix characteristics have been monitored by deuterium (2H) NMR spectroscopy as functions of the pH and lipid bilayer composition. The disordered multistate behavior of the (Glu, Arg)-containing helix varies with the lipid bilayer thickness and pH. The results highlight a fundamental induction of protein multistate properties by a single Glu residue in a lipid membrane environment.
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9
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Lomize AL, Schnitzer KA, Todd SC, Pogozheva ID. Thermodynamics-Based Molecular Modeling of α-Helices in Membranes and Micelles. J Chem Inf Model 2021; 61:2884-2896. [PMID: 34029472 DOI: 10.1021/acs.jcim.1c00161] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Folding of Membrane-Associated Peptides (FMAP) method was developed for modeling α-helix formation by linear peptides in micelles and lipid bilayers. FMAP 2.0 identifies locations of α-helices in the amino acid sequence, generates their three-dimensional models in planar bilayers or spherical micelles, and estimates their thermodynamic stabilities and tilt angles, depending on temperature and pH. The method was tested for 723 peptides (926 data points) experimentally studied in different environments and for 170 single-pass transmembrane (TM) proteins with available crystal structures. FMAP 2.0 detected more than 95% of experimentally observed α-helices with an average error in helix end determination of around 2, 3, 4, and 5 residues per helix for peptides in water, micelles, bilayers, and TM proteins, respectively. Helical and nonhelical residue states were predicted with an accuracy from 0.86 to 0.96, and the Matthews correlation coefficient was from 0.64 to 0.88 depending on the environment. Experimental micelle- and membrane-binding energies and tilt angles of peptides were reproduced with a root-mean-square deviation of around 2 kcal/mol and 7°, respectively. The TM and non-TM states of hydrophobic and pH-triggered α-helical peptides in various lipid bilayers were reproduced in more than 95% of cases. The FMAP 2.0 web server (https://membranome.org/fmap) is publicly available to explore the structural polymorphism of antimicrobial, cell-penetrating, fusion, and other membrane-binding peptides, which is important for understanding the mechanisms of their biological activities.
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Affiliation(s)
- Andrei L Lomize
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 428 Church Street, Ann Arbor, Michigan 48109-1065, United States
| | - Kevin A Schnitzer
- Department of Electrical Engineering and Computer Science, College of Engineering, University of Michigan, 1221 Beal Avenue, Ann Arbor, Michigan 48109-2102, United States
| | - Spencer C Todd
- Department of Electrical Engineering and Computer Science, College of Engineering, University of Michigan, 1221 Beal Avenue, Ann Arbor, Michigan 48109-2102, United States
| | - Irina D Pogozheva
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 428 Church Street, Ann Arbor, Michigan 48109-1065, United States
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10
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McKay M, Marr KA, Price JR, Greathouse DV, Koeppe RE. Lipid-Dependent Titration of Glutamic Acid at a Bilayer Membrane Interface. ACS OMEGA 2021; 6:8488-8494. [PMID: 33817510 PMCID: PMC8015139 DOI: 10.1021/acsomega.1c00276] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 03/08/2021] [Indexed: 06/12/2023]
Abstract
The ionization properties of protein side chains in lipid-bilayer membranes will differ from the canonical values of side chains exposed to an aqueous solution. While the propensities of positively charged side chains of His, Lys, and Arg to release a proton in lipid membranes have been rather well characterized, the propensity for a negatively charged Glu side chain to receive a proton and achieve the neutral state in a bilayer membrane has been less well characterized. Indeed, the ionization of the glutamic acid side chain has been predicted to depend on its depth of burial in a lipid membrane but has been difficult to verify experimentally. To address the issue, we incorporated an interfacial Glu residue at position 4 of a distinct 23-residue transmembrane helix and used 2H NMR to examine the helix properties as a function of pH. We observe that the helix tilt and azimuthal rotation vary little with pH, but the extent of helix unraveling near residues 3 and 4 changes as the Glu residue E4 titrates. Remarkably, the 2H quadrupolar splitting for the side chain of alanine A3 responds to pH with an apparent pK a of 4.8 in 1,2-dilauroyl-sn-glycero-3-phosphocholine (DLPC) and 6.3 in 1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine (DMPC), but is unchanged up to pH 8.0 in 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) in the presence of residue E4. With bilayers composed of alkali-stable ether-linked lipids, the side chain of A3 responds to pH with an apparent pK a of 11.0 in the ether analogue of DOPC. These results suggest that the depth dependence of Glu ionization in lipid-bilayer membranes may be steeper than previously predicted or envisioned.
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11
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Lapin J, Awosanya EO, Esteves RJA, Nevzorov AA. 1H/ 13C/ 15N triple-resonance experiments for structure determinaton of membrane proteins by oriented-sample NMR. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2021; 111:101701. [PMID: 33260039 DOI: 10.1016/j.ssnmr.2020.101701] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 11/13/2020] [Indexed: 06/12/2023]
Abstract
The benefits of triple-resonance experiments for structure determination of macroscopically oriented membrane proteins by solid-state NMR are discussed. While double-resonance 1H/15N experiments are effective for structure elucidation of alpha-helical domains, extension of the method of oriented samples to more complex topologies and assessing side-chain conformations necessitates further development of triple-resonance (1H/13C/15N) NMR pulse sequences. Incorporating additional spectroscopic dimensions involving 13C spin-bearing nuclei, however, introduces essential complications arising from the wide frequency range of the 1H-13C dipolar couplings and 13C CSA (>20 kHz), and the presence of the 13C-13C homonuclear dipole-dipole interactions. The recently reported ROULETTE-CAHA pulse sequence, in combination with the selective z-filtering, can be used to evolve the structurally informative 1H-13C dipolar coupling arising from the aliphatic carbons while suppressing the signals from the carbonyl and methyl regions. Proton-mediated magnetization transfer under mismatched Hartman-Hahn conditions (MMHH) can be used to correlate 13C and 15N nuclei in such triple-resonance experiments for the subsequent 15N detection. The recently developed pulse sequences are illustrated for n-acetyl Leucine (NAL) single crystal and doubly labeled Pf1 coat protein reconstituted in magnetically aligned bicelles. An interesting observation is that in the case of 15N-labeled NAL measured at 13C natural abundance, the triple (1H/13C/15N) MMHH scheme predominantly gives rise to long-range intermolecular magnetization transfers from 13C to 15N spins; whereas direct Hartmann-Hahn 13C/15N transfer is entirely intramolecular. The presented developments advance NMR of oriented samples for structure determination of membrane proteins and liquid crystals.
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Affiliation(s)
- Joel Lapin
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, NC, 27695-8204 USA
| | - Emmanuel O Awosanya
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, NC, 27695-8204 USA
| | - Richard J A Esteves
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, NC, 27695-8204 USA
| | - Alexander A Nevzorov
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, NC, 27695-8204 USA.
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12
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Targeting the transmembrane domain 5 of latent membrane protein 1 using small molecule modulators. Eur J Med Chem 2021; 214:113210. [PMID: 33550183 DOI: 10.1016/j.ejmech.2021.113210] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 01/14/2021] [Accepted: 01/14/2021] [Indexed: 12/16/2022]
Abstract
Protein-protein interactions (PPIs) play a critical role in living cells and represent promising targets for the drug discovery and life sciences communities. However, lateral transmembrane PPIs are difficult targets for small-molecule inhibitor development given less structural information is known and fewer ligand discovery methods have been explored compared to soluble proteins. In this study, the interactions of the transmembrane domain 5 (TMD-5) of latent membrane protein 1 (LMP-1) of Epstein-Barr virus (EBV) were disrupted by pentamidine derivatives to curb the committed step of EBV infection. A pentamidine derivative 2 with a 7-atom di-amide linker had the best activity whilst switching the amide regiochemistry in the linker influenced membrane permeability and abolished anti TMD-5 activity. Molecular dynamics simulations were performed to understand the interaction between pentamidine derivatives and TMD-5, and to rationalise the observed structure-activity relationships. This study explicitly demonstrated that the interaction of small molecule with lipid should be considered alongside interaction with the protein target when designing small molecules targeting the PPIs of TMDs. In all, this study provides proof of concept for the rational design of small molecules targeting transmembrane PPIs.
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13
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In Silico Prediction of the Binding, Folding, Insertion, and Overall Stability of Membrane-Active Peptides. Methods Mol Biol 2021; 2315:161-182. [PMID: 34302676 DOI: 10.1007/978-1-0716-1468-6_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Membrane-active peptides (MAPs) are short-length peptides used for potential biomedical applications in diagnostic imaging of tissues, targeted drug delivery, gene delivery, and antimicrobials and antibiotics. The broad appeal of MAPs is that they are infinitely variable, relatively low cost, and biocompatible. However, experimentally characterizing the specific properties of a MAP or its many variants is a low-resolution and potentially time-consuming endeavor; molecular dynamics (MD) simulations have emerged as an invaluable tool in identifying the biophysical interactions that are fundamental to the function of MAPs. In this chapter, a step-by-step approach to discreetly model the binding, folding, and insertion of a membrane-active peptide to a model lipid bilayer using MD simulations is described. Detailed discussion is devoted to the critical aspects of running these types of simulations: prior knowledge of the system, understanding the strengths and weaknesses of molecular mechanics force fields, proper construction and equilibration of the system, realistically estimating both experimental and computational timescales, and leveraging analysis to make direct comparisons to experimental results as often as possible.
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14
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Afrose F, Martfeld AN, Greathouse DV, Koeppe RE. Examination of pH dependency and orientation differences of membrane spanning alpha helices carrying a single or pair of buried histidine residues. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1863:183501. [PMID: 33130099 DOI: 10.1016/j.bbamem.2020.183501] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 10/22/2020] [Accepted: 10/23/2020] [Indexed: 01/08/2023]
Abstract
We have employed the peptide framework of GWALP23 (acetyl-GGALWLALALALALALALWLAGA-amide) to examine the orientation, dynamics and pH dependence of peptides having buried single or pairs of histidine residues. When residue L8 is substituted to yield GWALP23-H8, acetyl-GGALWLAH8ALALALALALWLAGA-amide, the deuterium NMR spectra of 2H-labeled core alanine residues reveal a helix that occupies a single transmembrane orientation in DLPC, or in DMPC at low pH, yet shows multiple states at higher pH or in bilayers of DOPC. Moreover, a single histidine at position 8 or 16 in the GWALP23 framework is sensitive to pH. Titration points are observed near pH 3.5 for the deprotonation of H8 in lipid bilayers of DLPC or DMPC, and for H16 in DOPC. When residues L8 and L16 both are substituted to yield GWALP23-H8,16, the 2H NMR spectra show, interestingly, no titration dependence from pH 2-8, yet bilayer thickness-dependent orientation differences. The helix with H8 and H16 is found to adopt a transmembrane orientation in thin bilayers of DLPC, a combination of transmembrane and surface orientations in DMPC, and then a complete transition to a surface bound orientation in the thicker DPoPC and DOPC lipid bilayers. In the surface orientations, alanine A7 no longer fits within the core helix. These results along with previous studies with different locations of histidine residues suggest that lipid hydrophobic thickness is a first determinant and pH a second determinant for the helical orientation, along with possible side-chain snorkeling, when the His residues are incorporated into the hydrophobic region of a lipid membrane-associated helix.
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Affiliation(s)
- Fahmida Afrose
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Ashley N Martfeld
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Denise V Greathouse
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Roger E Koeppe
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA.
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15
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Jones AJY, Gabriel F, Tandale A, Nietlispach D. Structure and Dynamics of GPCRs in Lipid Membranes: Physical Principles and Experimental Approaches. Molecules 2020; 25:E4729. [PMID: 33076366 PMCID: PMC7587580 DOI: 10.3390/molecules25204729] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/11/2020] [Accepted: 10/12/2020] [Indexed: 02/06/2023] Open
Abstract
Over the past decade, the vast amount of information generated through structural and biophysical studies of GPCRs has provided unprecedented mechanistic insight into the complex signalling behaviour of these receptors. With this recent information surge, it has also become increasingly apparent that in order to reproduce the various effects that lipids and membranes exert on the biological function for these allosteric receptors, in vitro studies of GPCRs need to be conducted under conditions that adequately approximate the native lipid bilayer environment. In the first part of this review, we assess some of the more general effects that a membrane environment exerts on lipid bilayer-embedded proteins such as GPCRs. This is then followed by the consideration of more specific effects, including stoichiometric interactions with specific lipid subtypes. In the final section, we survey a range of different membrane mimetics that are currently used for in vitro studies, with a focus on NMR applications.
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Affiliation(s)
| | | | | | - Daniel Nietlispach
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK; (A.J.Y.J.); (F.G.); (A.T.)
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16
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Mechanism of protein cleavage at asparagine leading to protein-protein cross-links. Biochem J 2020; 476:3817-3834. [PMID: 31794011 DOI: 10.1042/bcj20190743] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 12/01/2019] [Accepted: 12/03/2019] [Indexed: 12/21/2022]
Abstract
Long-lived proteins (LLPs) are present in numerous tissues within the human body. With age, they deteriorate, often leading to the formation of irreversible modifications such as peptide bond cleavage and covalent cross-linking. Currently understanding of the mechanism of formation of these cross-links is limited. As part of an ongoing study, proteomics was used to characterise sites of novel covalent cross-linking in the human lens. In this process, Lys residues were found cross-linked to C-terminal aspartates that had been present in the original protein as Asn residues. Cross-links were identified in major lens proteins such as αA-crystallin, αB-crystallin and aquaporin 0. Quantification of the level of an AQP0/AQP0 cross-linked peptide showed increased cross-linking with age and in cataract lenses. Using model peptides, a mechanism of cross-link formation was elucidated that involves spontaneous peptide bond cleavage on the C-terminal side of Asn residues resulting in the formation of a C-terminal succinimide. This succinimide does not form cross-links, but can hydrolyse to a mixture of C-terminal Asn and C-terminal Asp amide peptides. The C-terminal Asp amide is unstable at neutral pH and decomposes to a succinic anhydride. If the side chain of Lys attacks the anhydride, a covalent cross-link will be formed. This multi-step mechanism represents a link between two spontaneous events: peptide bond cleavage at Asn and covalent cross-linking. Since Asn deamidation and cleavage are abundant age-related modifications in LLPs, this finding suggests that such susceptible Asn residues should also be considered as potential sites for spontaneous covalent cross-linking.
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17
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Sepehri A, PeBenito L, Pino-Angeles A, Lazaridis T. What Makes a Good Pore Former: A Study of Synthetic Melittin Derivatives. Biophys J 2020; 118:1901-1913. [PMID: 32183940 DOI: 10.1016/j.bpj.2020.02.024] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 01/25/2020] [Accepted: 02/12/2020] [Indexed: 12/15/2022] Open
Abstract
Pore formation by membrane-active peptides, naturally encountered in innate immunity and infection, could have important medical and technological applications. Recently, the well-studied lytic peptide melittin has formed the basis for the development of combinatorial libraries from which potent pore-forming peptides have been derived, optimized to work under different conditions. We investigate three such peptides, macrolittin70, which is most active at neutral pH; pHD15, which is active only at low pH; and MelP5_Δ6, which was rationally designed to be active at low pH but formed only small pores. There are three, six, and six acidic residues in macrolittin70, pHD15, and MelP5_Δ6, respectively. We perform multi-microsecond simulations in 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) of hexamers of these peptides starting from transmembrane orientations at neutral pH (all residues at standard protonation), low pH (acidic residues and His protonated), and highly acidic environments in which C-termini are also protonated. Previous simulations of the parent peptides melittin and MelP5 in 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) are repeated in POPC. We find that the most potent pore-forming peptides exhibit strong interpeptide interactions, including salt bridges, H-bonds, and polar interactions. Protonation of the C-terminus promotes helicity and pore size. The proximity of the peptides allows fewer lipid headgroups to line the pores than in previous simulations, making the pores intermediate between barrel stave and toroidal. Based on these structures and geometrical arguments, we attempt to rationalize the factors that under different conditions can increase or decrease pore stability and propose mutations that could be tested experimentally.
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Affiliation(s)
- Aliasghar Sepehri
- Department of Chemistry & Biochemistry, The City College of New York, New York, New York
| | - Leo PeBenito
- Department of Chemistry & Biochemistry, The City College of New York, New York, New York; Graduate Program in Chemistry, The Graduate Center, City University of New York, New York, New York
| | - Almudena Pino-Angeles
- Department of Chemistry & Biochemistry, The City College of New York, New York, New York
| | - Themis Lazaridis
- Department of Chemistry & Biochemistry, The City College of New York, New York, New York; Graduate Program in Chemistry, The Graduate Center, City University of New York, New York, New York.
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18
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Comparing Interfacial Trp, Interfacial His and pH Dependence for the Anchoring of Tilted Transmembrane Helical Peptides. Biomolecules 2020; 10:biom10020273. [PMID: 32053887 PMCID: PMC7072424 DOI: 10.3390/biom10020273] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 02/07/2020] [Accepted: 02/10/2020] [Indexed: 11/27/2022] Open
Abstract
Charged and aromatic amino acid residues, being enriched toward the terminals of membrane-spanning helices in membrane proteins, help to stabilize particular transmembrane orientations. Among them, histidine is aromatic and can be positively charge at low pH. To enable investigations of the underlying protein-lipid interactions, we have examined the effects of single or pairs of interfacial histidine residues using the constructive low-dynamic GWALP23 (acetyl-GG2ALW5LALALALALALALW19LAG22A-amide) peptide framework by incorporating individual or paired histidines at locations 2, 5, 19 or 22. Analysis of helix orientation by means of solid-state 2H NMR spectra of labeled alanine residues reveals marked differences with H2,22 compared to W2,22. Nevertheless, the properties of membrane-spanning H2,22WALP23 helices show little pH dependence and are similar to those having Gly, Arg or Lys at positions 2 and 22. The presence of H5 or H19 influences the helix rotational preference but not the tilt magnitude. H5 affects the helical integrity, as residue 7 unwinds from the core helix; yet once again the helix orientation and dynamic properties show little sensitivity to pH. The overall results reveal that the detailed properties of transmembrane helices depend upon the precise locations of interfacial histidine residues.
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19
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Influence of interfacial tryptophan residues on an arginine-flanked transmembrane helix. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183134. [PMID: 31738898 DOI: 10.1016/j.bbamem.2019.183134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 10/31/2019] [Accepted: 11/01/2019] [Indexed: 10/25/2022]
Abstract
The transmembrane helices of membrane proteins often are flanked by interfacial charged or aromatic residues that potentially help to anchor the membrane-spanning protein. For isolated single-span helices, the interfacial residues may be especially important for stabilizing particular tilted transmembrane orientations. The peptide RWALP23 (acetyl-GR2ALW(LA)6LWLAR22A-amide) has been employed to investigate the interplay between interfacial arginines and tryptophans. Here we replace the tryptophans of RWALP23 with A5 and A19, to investigate arginines alone with respect to helix fraying and orientation in varying lipid bilayers. Deuterated alanines incorporated into the central sequence allow the orientation and stability of the core helix to be assessed by means of solid -state 2H NMR in bilayers of DOPC, DMPC and DLPC. The helix tilt from the bilayer normal is found to increase slightly when R2 and R22 are present, and increases still further when the tryptophans W5 and W19 are replaced by alanines. The extent of helix dynamic averaging remains low in all cases. The preferred helix azimuthal rotation is essentially constant for all of the helices in each of the lipid membranes considered here. The alanines located outside of the core region of the peptide are sensitive to helical integrity. The new alanines, A5 and A19, therefore, provide new information about the length of the core helix and the onset of unraveling of the terminals. Residue A19 remains essentially on the central helix in each lipid membrane, while residues A3, A5 and A21 deviate from the core helix to an extent that depends on the membrane thickness. Differential unraveling of the two ends to expose peptide backbone groups for hydrogen bonding therefore acts together with specific interfacial side chains to stabilize a transmembrane helix.
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20
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Awosanya EO, Lapin J, Nevzorov AA. NMR "Crystallography" for Uniformly ( 13 C, 15 N)-Labeled Oriented Membrane Proteins. Angew Chem Int Ed Engl 2020; 59:3554-3557. [PMID: 31887238 DOI: 10.1002/anie.201915110] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 12/29/2019] [Indexed: 01/01/2023]
Abstract
In oriented-sample (OS) solid-state NMR of membrane proteins, the angular-dependent dipolar couplings and chemical shifts provide a direct input for structure calculations. However, so far only 1 H-15 N dipolar couplings and 15 N chemical shifts have been routinely assessed in oriented 15 N-labeled samples. The main obstacle for extending this technique to membrane proteins of arbitrary topology has remained in the lack of additional experimental restraints. We have developed a new experimental triple-resonance NMR technique, which was applied to uniformly doubly (15 N, 13 C)-labeled Pf1 coat protein in magnetically aligned DMPC/DHPC bicelles. The previously inaccessible 1 Hα -13 Cα dipolar couplings have been measured, which make it possible to determine the torsion angles between the peptide planes without assuming α-helical structure a priori. The fitting of three angular restraints per peptide plane and filtering by Rosetta scoring functions has yielded a consensus α-helical transmembrane structure for Pf1 protein.
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Affiliation(s)
- Emmanuel O Awosanya
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, NC, 27695-8204, USA
| | - Joel Lapin
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, NC, 27695-8204, USA
| | - Alexander A Nevzorov
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, NC, 27695-8204, USA
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21
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Awosanya EO, Lapin J, Nevzorov AA. NMR “Crystallography” for Uniformly (
13
C,
15
N)‐Labeled Oriented Membrane Proteins. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201915110] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Emmanuel O. Awosanya
- Department of Chemistry North Carolina State University 2620 Yarbrough Drive Raleigh NC 27695-8204 USA
| | - Joel Lapin
- Department of Chemistry North Carolina State University 2620 Yarbrough Drive Raleigh NC 27695-8204 USA
| | - Alexander A. Nevzorov
- Department of Chemistry North Carolina State University 2620 Yarbrough Drive Raleigh NC 27695-8204 USA
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22
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Ermilova I, Lyubartsev AP. Modelling of interactions between Aβ(25-35) peptide and phospholipid bilayers: effects of cholesterol and lipid saturation. RSC Adv 2020; 10:3902-3915. [PMID: 35492630 PMCID: PMC9048594 DOI: 10.1039/c9ra06424a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 12/14/2019] [Indexed: 11/25/2022] Open
Abstract
Aggregation of amyloid beta (Aβ) peptides in neuronal membranes is a known promoter of Alzheimer’s disease. To gain insight into the molecular details of Aβ peptide aggregation and its effect on model neuronal membranes, we carried out molecular dynamics simulations of the Aβ(25–35) fragment of the amyloid precursor protein in phospholipid bilayers composed of either fully saturated or highly unsaturated lipids, in the presence or absence of cholesterol. It was found that the peptide does not penetrate through any of the considered membranes, but can reside in the headgroup region and upper part of the lipid tails showing a clear preference to a polyunsaturated cholesterol-free membrane. Due to the ordering and condensing effect upon addition of cholesterol, membranes become more rigid facilitating peptide aggregation on the surface. Except for the case of the cholesterol-free saturated lipid bilayer, the peptides have a small effect on the membrane structure and ordering. It was also found that the most “active” amino-acid for peptide–lipid and peptide–cholesterol interaction is methionine-35, followed by asparagine-27 and serine-26, which form hydrogen bonds between peptides and polar atoms of lipid headgroups. These amino acids are also primarily responsible for peptide aggregation. This work will be relevant for designing strategies to develop drugs to combat Alzheimer’s disease. Molecular dynamics simulations of Aβ(25–35) peptides in phospholipid bilayers are carried out to investigate the effect of polyunsaturated lipids and cholesterol on aggregation of the peptides. ![]()
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Affiliation(s)
- Inna Ermilova
- Department of Materials and Environmental Chemistry, Stockholm University Stockholm Sweden +46 8161193
| | - Alexander P Lyubartsev
- Department of Materials and Environmental Chemistry, Stockholm University Stockholm Sweden +46 8161193
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23
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Marshall SR, Stoudt ML, DiVittorio MA, Sargent AL, Allen WE. Side-Chain Protonation States of a Fluorescent Arginine. J Org Chem 2019; 84:14407-14413. [PMID: 31608637 DOI: 10.1021/acs.joc.9b00677] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An arginine derivative with a fluorescent side-chain, Boc-Arg(Nap)-OH, was prepared by palladium(0)-catalyzed coupling of Boc-Arg-OH with a 4-bromonaphthalimide. The presence of the fluorophore lowers the pKa of the side-chain guanidinium group by several orders of magnitude, to 9.0 (±0.1), allowing the derivative to access an electrically neutral protonation state that is not generally available to arginine itself. Computational modeling (DFT) predicts that protonation takes place at the side-chain C═N atom that bears the fluorophore. Calculated electronic absorptions for the protonated (356 nm) and neutral species (440 nm) are in good agreement with experiment. When irradiated with light, excited-state proton transfer (ESPT) occurs from cationic side-chains to suitably basic solvents, resulting in fluorescence emission from the neutral species. Arg(Nap) can be incorporated into peptides with sterically accessible N-termini using specially adapted conditions of solid-phase peptide synthesis.
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Affiliation(s)
- Sarah R Marshall
- Department of Chemistry, Science and Technology Building , East Carolina University , Greenville , North Carolina 27858-4353 , United States
| | - Mikayla L Stoudt
- Department of Chemistry, Science and Technology Building , East Carolina University , Greenville , North Carolina 27858-4353 , United States
| | - Madeleine A DiVittorio
- Department of Chemistry, Science and Technology Building , East Carolina University , Greenville , North Carolina 27858-4353 , United States
| | - Andrew L Sargent
- Department of Chemistry, Science and Technology Building , East Carolina University , Greenville , North Carolina 27858-4353 , United States
| | - William E Allen
- Department of Chemistry, Science and Technology Building , East Carolina University , Greenville , North Carolina 27858-4353 , United States
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24
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Salvage SC, Zhu W, Habib ZF, Hwang SS, Irons JR, Huang CLH, Silva JR, Jackson AP. Gating control of the cardiac sodium channel Nav1.5 by its β3-subunit involves distinct roles for a transmembrane glutamic acid and the extracellular domain. J Biol Chem 2019; 294:19752-19763. [PMID: 31659116 PMCID: PMC6926464 DOI: 10.1074/jbc.ra119.010283] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 10/24/2019] [Indexed: 11/06/2022] Open
Abstract
The auxiliary β3-subunit is an important functional regulator of the cardiac sodium channel Nav1.5, and some β3 mutations predispose individuals to cardiac arrhythmias. The β3-subunit uses its transmembrane α-helix and extracellular domain to bind to Nav1.5. Here, we investigated the role of an unusually located and highly conserved glutamic acid (Glu-176) within the β3 transmembrane region and its potential for functionally synergizing with the β3 extracellular domain (ECD). We substituted Glu-176 with lysine (E176K) in the WT β3-subunit and in a β3-subunit lacking the ECD. Patch-clamp experiments indicated that the E176K substitution does not affect the previously observed β3-dependent depolarizing shift of V½ of steady-state inactivation but does attenuate the accelerated recovery from inactivation conferred by the WT β3-subunit. Removal of the β3-ECD abrogated both the depolarizing shift of steady-state inactivation and the accelerated recovery, irrespective of the presence or absence of the Glu-176 residue. We found that steady-state inactivation and recovery from inactivation involve movements of the S4 helices within the DIII and DIV voltage sensors in response to membrane potential changes. Voltage-clamp fluorometry revealed that the E176K substitution alters DIII voltage sensor dynamics without affecting DIV. In contrast, removal of the ECD significantly altered the dynamics of both DIII and DIV. These results imply distinct roles for the β3-Glu-176 residue and the β3-ECD in regulating the conformational changes of the voltage sensors that determine channel inactivation and recovery from inactivation.
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Affiliation(s)
- Samantha C Salvage
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom
| | - Wandi Zhu
- Department of Biomedical Engineering, Washington University, St. Louis, Missouri 63130-489
| | - Zaki F Habib
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom.,Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, United Kingdom
| | - Soyon S Hwang
- Department of Biomedical Engineering, Washington University, St. Louis, Missouri 63130-489
| | - Jennifer R Irons
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom
| | - Christopher L H Huang
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom .,Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, United Kingdom
| | - Jonathan R Silva
- Department of Biomedical Engineering, Washington University, St. Louis, Missouri 63130-489
| | - Antony P Jackson
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom
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25
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Lipinski K, McKay MJ, Afrose F, Martfeld AN, Koeppe RE, Greathouse DV. Influence of Lipid Saturation, Hydrophobic Length and Cholesterol on Double-Arginine-Containing Helical Peptides in Bilayer Membranes. Chembiochem 2019; 20:2784-2792. [PMID: 31150136 DOI: 10.1002/cbic.201900282] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Indexed: 12/12/2022]
Abstract
Membrane proteins are essential for many cell processes yet are more difficult to investigate than soluble proteins. Charged residues often contribute significantly to membrane protein function. Model peptides such as GWALP23 (acetyl-GGALW5 LAL8 LALALAL16 ALW19 LAGA-amide) can be used to characterize the influence of specific residues on transmembrane protein domains. We have substituted R8 and R16 in GWALP23 in place of L8 and L16, equidistant from the peptide center, and incorporated specific 2 H-labeled alanine residues within the central sequence for detection by solid-state 2 H NMR spectroscopy. The resulting pattern of [2 H]Ala quadrupolar splitting (Δνq ) magnitudes indicates the core helix for R8,16 GWALP23 is significantly tilted to give a similar transmembrane orientation in thinner bilayers with either saturated C12:0 or C14:0 acyl chains (1,2-dilauroyl-sn-glycero-3-phosphocholine (DLPC) or 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC)) or unsaturated C16:1 Δ9 cis acyl chains. In bilayers of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC; C18:1 Δ9 cis) multiple orientations are indicated, whereas in longer, unsaturated 1,2-dieicosenoyl-sn-glycero-3-phosphocholine (DEiPC; C20:1 Δ11 cis) bilayers, the R8,16 GWALP23 helix adopts primarily a surface orientation. The inclusion of 10-20 mol % cholesterol in DOPC bilayers drives more of the R8,16 GWALP23 helix population to the membrane surface, thereby allowing both charged arginines access to the interfacial lipid head groups. The results suggest that hydrophobic thickness and cholesterol content are more important than lipid saturation for the arginine peptide dynamics and helix orientation in lipid membranes.
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Affiliation(s)
- Karli Lipinski
- Department of Chemistry and Biochemistry, University of Arkansas, 119 Chemistry Building, Fayetteville, AR, 72701, USA
| | - Matthew J McKay
- Department of Chemistry and Biochemistry, University of Arkansas, 119 Chemistry Building, Fayetteville, AR, 72701, USA
| | - Fahmida Afrose
- Department of Chemistry and Biochemistry, University of Arkansas, 119 Chemistry Building, Fayetteville, AR, 72701, USA
| | - Ashley N Martfeld
- Department of Chemistry and Biochemistry, University of Arkansas, 119 Chemistry Building, Fayetteville, AR, 72701, USA.,Present address: Department Department of Neurobiology, Duke University Medical Center, 311 Research Drive, Durham, NC, 27710, USA
| | - Roger E Koeppe
- Department of Chemistry and Biochemistry, University of Arkansas, 119 Chemistry Building, Fayetteville, AR, 72701, USA
| | - Denise V Greathouse
- Department of Chemistry and Biochemistry, University of Arkansas, 119 Chemistry Building, Fayetteville, AR, 72701, USA
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26
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McKay MJ, Fu R, Greathouse DV, Koeppe RE. Breaking the Backbone: Central Arginine Residues Induce Membrane Exit and Helix Distortions within a Dynamic Membrane Peptide. J Phys Chem B 2019; 123:8034-8047. [PMID: 31483653 DOI: 10.1021/acs.jpcb.9b06034] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Transmembrane domains of membrane proteins sometimes contain conserved charged or ionizable residues which may be essential for protein function and regulation. This work examines the molecular interactions of single Arg residues within a highly dynamic transmembrane peptide helix. To this end, we have modified the GW4,20ALP23 (acetyl-GGAW4(AL)7AW20AGA-amide) model peptide framework to incorporate Arg residues near the center of the peptide. Peptide helix formation, orientation and dynamics were analyzed by means of solid-state NMR spectroscopy to monitor specific 2H- or 15N-labeled residues. GW4,20ALP23 itself adopts a tilted orientation within lipid bilayer membranes. Nevertheless, the GW4,20ALP23 helix exhibits moderate to high dynamic averaging of NMR observables, such as 2H quadrupolar splittings or 15N-1H dipolar couplings, due to competition between the interfacial Trp residues on opposing helix faces. Here we examine how the helix dynamics are impacted by the introduction of a single Arg residue at position 12 or 14. Residue R14 restricts the helix to low dynamic averaging and a well-defined tilt that varies inversely with the lipid bilayer thickness. To compensate for the dominance of R14, the competing Trp residues cause partial unwinding of the helix at the C-terminal. By contrast, R12GW4,20ALP23 exits the DOPC bilayer to an interfacial surface-bound location. Interestingly, multiple orientations are exhibited by a single residue, Ala-9. Quadrupolar splittings generated by 2H-labeled residues A3, A5, A7, and A9 do not fit to the α-helical quadrupolar wave plot defined by residues A11, A13, A15, A17, A19, and A21. The discontinuity at residue A9 implicates a helical swivel distortion and an apparent 310-helix involving the N-terminal residues preceding A11. These molecular features suggest that, while arginine residues are prominent factors controlling transmembrane helix dynamics, the influence of interfacial tryptophan residues cannot be ignored.
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Affiliation(s)
- Matthew J McKay
- Department of Chemistry and Biochemistry , University of Arkansas , Fayetteville , Arkansas 72701 , United States
| | - Riqiang Fu
- National High Magnetic Field Laboratory, Florida State University , Tallahassee , Florida 32310 , 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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27
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Situ AJ, Ulmer TS. Universal principles of membrane protein assembly, composition and evolution. PLoS One 2019; 14:e0221372. [PMID: 31415673 PMCID: PMC6695178 DOI: 10.1371/journal.pone.0221372] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 08/05/2019] [Indexed: 11/18/2022] Open
Abstract
Structural diversity in α-helical membrane proteins (MP) arises from variations in helix-helix crossings and contacts that may bias amino acid usage. Here, we reveal systematic changes in transmembrane amino acid frequencies (f) as a function of the number of helices (n). For eukarya, breaks in f(n) trends of packing (Ala, Gly and Pro), polar, and hydrophobic residues identify different MP assembly principles for 2≤n≤7, 8≤n≤12 and n≥13. In bacteria, the first f break already occurs after n = 6 in correlation to an earlier n peak in MP size distribution and dominance of packing over polar interactions. In contrast to the later n brackets, the integration levels of helix bundles continuously increased in the first, most populous brackets indicating the formation of single structural units (domains). The larger first bracket of eukarya relates to a balance of polar and packing interactions that enlarges helix-helix combinatorial possibilities (MP diversity). Between the evolutionary old, packing and new, polar residues f anti-correlations extend over all biological taxa, broadly ordering them according to evolutionary history and allowing f estimates for the earliest forms of life. Next to evolutionary history, the amino acid composition of MP is determined by size (n), proteome diversity, and effective amino acid cost.
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Affiliation(s)
- Alan J. Situ
- Department of Physiology and Neuroscience, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States of America
| | - Tobias S. Ulmer
- Department of Physiology and Neuroscience, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States of America
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States of America
- * E-mail:
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28
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Lapin J, Nevzorov AA. Validation of protein backbone structures calculated from NMR angular restraints using Rosetta. JOURNAL OF BIOMOLECULAR NMR 2019; 73:229-244. [PMID: 31076969 DOI: 10.1007/s10858-019-00251-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Accepted: 05/02/2019] [Indexed: 06/09/2023]
Abstract
Multidimensional solid-state NMR spectra of oriented membrane proteins can be used to infer the backbone torsion angles and hence the overall protein fold by measuring dipolar couplings and chemical shift anisotropies, which depend on the orientation of each peptide plane with respect to the external magnetic field. However, multiple peptide plane orientations can be consistent with a given set of angular restraints. This ambiguity is further exacerbated by experimental uncertainty in obtaining and interpreting such restraints. The previously developed algorithms for structure calculations using angular restraints typically involve a sequential walkthrough along the backbone to find the torsion angles between the consecutive peptide plane orientations that are consistent with the experimental data. This method is sensitive to experimental uncertainty in interpreting the peak positions of as low as ± 10 Hz, often yielding high structural RMSDs for the calculated structures. Here we present a significantly improved version of the algorithm which includes the fitting of several peptide planes at once in order to prevent propagation of error along the backbone. In addition, a protocol has been devised for filtering the structural solutions using Rosetta scoring functions in order to find the structures that both fit the spectrum and satisfy bioinformatics restraints. The robustness of the new algorithm has been tested using synthetic angular restraints generated from the known structures for two proteins: a soluble protein 2gb1 (56 residues), chosen for its diverse secondary structure elements, i.e. an alpha-helix and two beta-sheets, and a membrane protein 4a2n, from which the first two transmembrane helices (having a total of 64 residues) have been used. Extensive simulations have been performed by varying the number of fitted planes, experimental error, and the number of NMR dimensions. It has been found that simultaneously fitting two peptide planes always shifted the distribution of the calculated structures toward lower structural RMSD values as compared to fitting a single torsion-angle pair. For each protein, irrespective of the simulation parameters, Rosetta was able to distinguish the most plausible structures, often having structural RMSDs lower than 2 Å with respect to the original structure. This study establishes a framework for de-novo protein structure prediction using a combination of solid-state NMR angular restraints and bioinformatics.
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Affiliation(s)
- Joel Lapin
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, NC, 27695-8204, USA
| | - Alexander A Nevzorov
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, NC, 27695-8204, USA.
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29
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Dutta D, Ullah A, Bibi S, Fliegel L. Functional Analysis of Conserved Transmembrane Charged Residues and a Yeast Specific Extracellular Loop of the Plasma Membrane Na +/H + Antiporter of Schizosaccharomyces pombe. Sci Rep 2019; 9:6191. [PMID: 30996236 PMCID: PMC6470128 DOI: 10.1038/s41598-019-42658-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 04/01/2019] [Indexed: 01/20/2023] Open
Abstract
The Na+/H+ exchanger of the plasma membrane of S. pombe (SpNHE1) removes excess intracellular sodium in exchange for an extracellular proton. We examined the functional role of acidic amino acids of a yeast specific periplasmic extracellular loop 6 (EL6) and of Glu74 and Arg77 of transmembrane segment 3. Glu74 and Arg77 are conserved in yeast species while Glu74 is conserved throughout various phyla. The mutation E74A caused a minor effect, while mutation R77A had a larger effect on the ability of SpNHE1 to confer salt tolerance. Mutation of both residues to Ala or Glu also eliminated the ability to confer salt tolerance. Arg341 and Arg342 were also necessary for SpNHE1 transport in S. pombe. Deletion of 3 out of 4 acidic residues (Asp389, Glu390, Glu392, Glu397) of EL6 did not greatly affect SpNHE1 function while deletion of all did. Replacement of EL6 with a segment from the plant Na+/H+ exchanger SOS1 also did not affect function. We suggest that EL6 forms part of a cation coordination sphere, attracting cations for transport but that the region is not highly specific for the location of acidic charges. Overall, we identified a number of polar amino acids important in SpNHE1 function.
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Affiliation(s)
- Debajyoti Dutta
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, T6G 2H7, Canada
| | - Asad Ullah
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, T6G 2H7, Canada
| | - Sana Bibi
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, T6G 2H7, Canada
| | - Larry Fliegel
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, T6G 2H7, Canada.
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30
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Duay SS, Sharma G, Prabhakar R, Angeles-Boza AM, May ER. Molecular Dynamics Investigation into the Effect of Zinc(II) on the Structure and Membrane Interactions of the Antimicrobial Peptide Clavanin A. J Phys Chem B 2019; 123:3163-3176. [PMID: 30908921 DOI: 10.1021/acs.jpcb.8b11496] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Clavanin A (ClavA) is an antimicrobial peptide (AMP) whose antimicrobial activity is enhanced in the presence of Zn(II) ions. The antimicrobial activity of ClavA has been shown to increase 16-fold in the presence of Zn(II) ions. In this study, we investigate the potential sources of this enhancement, namely, the effect of Zn(II) binding on the helical conformation of ClavA and on the ClavA interaction with a model for gram-negative bacterial membranes. In addition, we investigate the effect of Zn(II) on the membrane mechanical properties. We employed all-atom equilibrium molecular dynamics simulations initiated from both fully helical and random coil structures of ClavA. We observe that Zn(II) can stabilize an existing helical conformation in the Zn(II)-binding region, but we do not observe induction of helical conformations in systems initiated in random coil configurations. Zn(II) binding to ClavA provides more favorable electrostatics for membrane association in the C-terminal region. This is evidenced by longer and stronger C-terminal-lipid interactions. Zn(II) is also capable of modulating the membrane properties in a manner which favors ClavA insertion and the potential for enhanced translocation into the cell. This work provides insights into the role of divalent metal cations in the antimicrobial activity of ClavA. This information can be used for the development of synthetic AMPs containing motifs that can bind metals (metalloAMPs) for therapeutic and medical purposes.
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Affiliation(s)
| | - Gaurav Sharma
- Department of Chemistry , University of Miami , Coral Gables , Florida 33146 , United States
| | - Rajeev Prabhakar
- Department of Chemistry , University of Miami , Coral Gables , Florida 33146 , United States
| | | | - Eric R May
- Department of Molecular and Cell Biology , University of Connecticut , 91 N. Eagleville Road , Storrs , Connecticut 06269 , United States
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31
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Enkavi G, Javanainen M, Kulig W, Róg T, Vattulainen I. Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance. Chem Rev 2019; 119:5607-5774. [PMID: 30859819 PMCID: PMC6727218 DOI: 10.1021/acs.chemrev.8b00538] [Citation(s) in RCA: 173] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
![]()
Biological
membranes are tricky to investigate. They are complex
in terms of molecular composition and structure, functional
over a wide range of time scales, and characterized
by nonequilibrium conditions. Because of all of these
features, simulations are a great technique to study biomembrane
behavior. A significant part of the functional processes
in biological membranes takes place at the molecular
level; thus computer simulations are the method of
choice to explore how their properties emerge from specific
molecular features and how the interplay among the numerous
molecules gives rise to function over spatial and
time scales larger than the molecular ones. In this
review, we focus on this broad theme. We discuss the current
state-of-the-art of biomembrane simulations that, until
now, have largely focused on a rather narrow picture
of the complexity of the membranes. Given this, we
also discuss the challenges that we should unravel in the
foreseeable future. Numerous features such as the actin-cytoskeleton
network, the glycocalyx network, and nonequilibrium
transport under ATP-driven conditions have so far
received very little attention; however, the potential
of simulations to solve them would be exceptionally high. A
major milestone for this research would be that one day
we could say that computer simulations genuinely research
biological membranes, not just lipid bilayers.
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Affiliation(s)
- Giray Enkavi
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland
| | - Matti Javanainen
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland.,Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Flemingovo naḿesti 542/2 , 16610 Prague , Czech Republic.,Computational Physics Laboratory , Tampere University , P.O. Box 692, FI-33014 Tampere , Finland
| | - Waldemar Kulig
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland
| | - Tomasz Róg
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland.,Computational Physics Laboratory , Tampere University , P.O. Box 692, FI-33014 Tampere , Finland
| | - Ilpo Vattulainen
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland.,Computational Physics Laboratory , Tampere University , P.O. Box 692, FI-33014 Tampere , Finland.,MEMPHYS-Center for Biomembrane Physics
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Pahuja KB, Nguyen TT, Jaiswal BS, Prabhash K, Thaker TM, Senger K, Chaudhuri S, Kljavin NM, Antony A, Phalke S, Kumar P, Mravic M, Stawiski EW, Vargas D, Durinck S, Gupta R, Khanna-Gupta A, Trabucco SE, Sokol ES, Hartmaier RJ, Singh A, Chougule A, Trivedi V, Dutt A, Patil V, Joshi A, Noronha V, Ziai J, Banavali SD, Ramprasad V, DeGrado WF, Bueno R, Jura N, Seshagiri S. Actionable Activating Oncogenic ERBB2/HER2 Transmembrane and Juxtamembrane Domain Mutations. Cancer Cell 2018; 34:792-806.e5. [PMID: 30449325 PMCID: PMC6248889 DOI: 10.1016/j.ccell.2018.09.010] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 07/26/2018] [Accepted: 09/24/2018] [Indexed: 02/08/2023]
Abstract
Deregulated HER2 is a target of many approved cancer drugs. We analyzed 111,176 patient tumors and identified recurrent mutations in HER2 transmembrane domain (TMD) and juxtamembrane domain (JMD) that include G660D, R678Q, E693K, and Q709L. Using a saturation mutagenesis screen and testing of patient-derived mutations we found several activating TMD and JMD mutations. Structural modeling and analysis showed that the TMD/JMD mutations function by improving the active dimer interface or stabilizing an activating conformation. Further, we found that HER2 G660D employed asymmetric kinase dimerization for activation and signaling. Importantly, anti-HER2 antibodies and small-molecule kinase inhibitors blocked the activity of TMD/JMD mutants. Consistent with this, a G660D germline mutant lung cancer patient showed remarkable clinical response to HER2 blockade.
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Affiliation(s)
- Kanika Bajaj Pahuja
- Molecular Biology Department, Genentech Inc., South San Francisco, CA 94080, USA
| | - Thong T Nguyen
- Molecular Biology Department, Genentech Inc., South San Francisco, CA 94080, USA
| | - Bijay S Jaiswal
- Molecular Biology Department, Genentech Inc., South San Francisco, CA 94080, USA
| | | | - Tarjani M Thaker
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA 94158, USA
| | - Kate Senger
- Molecular Biology Department, Genentech Inc., South San Francisco, CA 94080, USA
| | - Subhra Chaudhuri
- Molecular Biology Department, Genentech Inc., South San Francisco, CA 94080, USA
| | - Noelyn M Kljavin
- Molecular Oncology Department, Genentech Inc., South San Francisco, CA 94080, USA
| | - Aju Antony
- Department of Molecular Biology, SciGenom Labs, Cochin, Kerala 682037, India
| | - Sameer Phalke
- Research Division, MedGenome Labs Pvt. Ltd., Bangalore, Karnataka 560099, India
| | - Prasanna Kumar
- Research Division, MedGenome Labs Pvt. Ltd., Bangalore, Karnataka 560099, India
| | - Marco Mravic
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | - Eric W Stawiski
- Molecular Biology Department, Genentech Inc., South San Francisco, CA 94080, USA; Bioinformatics and Computational Biology Department, Genentech Inc., South San Francisco, CA 94080, USA
| | - Derek Vargas
- Research and Development Department, MedGenome Inc., Foster City, CA 94404, USA
| | - Steffen Durinck
- Molecular Biology Department, Genentech Inc., South San Francisco, CA 94080, USA; Bioinformatics and Computational Biology Department, Genentech Inc., South San Francisco, CA 94080, USA
| | - Ravi Gupta
- Bioinformatics Department, MeGenome Labs Pvt. Ltd., Bangalore, Karnataka 560099, India
| | - Arati Khanna-Gupta
- Research Division, MedGenome Labs Pvt. Ltd., Bangalore, Karnataka 560099, India
| | - Sally E Trabucco
- Foundation Medicine Inc., 150 Second Street, Cambridge, MA 02141, USA
| | - Ethan S Sokol
- Foundation Medicine Inc., 150 Second Street, Cambridge, MA 02141, USA
| | - Ryan J Hartmaier
- Foundation Medicine Inc., 150 Second Street, Cambridge, MA 02141, USA
| | - Ashish Singh
- Department of Medical Oncology, Christian Medical College and Hospital, Vellore 632004, India
| | | | | | - Amit Dutt
- ACTREC, Tata Memorial Centre, Navi Mumbai 410210, India; Homi Bhaba National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Vijay Patil
- Tata Memorial Hospital, Parel, Mumbai 400012, India
| | - Amit Joshi
- Tata Memorial Hospital, Parel, Mumbai 400012, India
| | | | - James Ziai
- Pathology Department, Genentech Inc., South San Francisco, CA 94080, USA
| | | | - Vedam Ramprasad
- Research Division, MedGenome Labs Pvt. Ltd., Bangalore, Karnataka 560099, India
| | - William F DeGrado
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | - Raphael Bueno
- Division of Thoracic Surgery, The Lung Center and the International Mesothelioma Program, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Natalia Jura
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Somasekar Seshagiri
- Molecular Biology Department, Genentech Inc., South San Francisco, CA 94080, USA.
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33
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Kaur G, Pati PK. In silico insights on diverse interacting partners and phosphorylation sites of respiratory burst oxidase homolog (Rbohs) gene families from Arabidopsis and rice. BMC PLANT BIOLOGY 2018; 18:161. [PMID: 30097007 PMCID: PMC6086027 DOI: 10.1186/s12870-018-1378-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 07/30/2018] [Indexed: 05/14/2023]
Abstract
BACKGROUND NADPH oxidase (Nox) is a critical enzyme involved in the generation of apoplastic superoxide (O2-), a type of reactive oxygen species (ROS) and hence regulate a wide range of biological functions in many organisms. Plant Noxes are the homologs of the catalytic subunit from mammalian NADPH oxidases and are known as respiratory burst oxidase homologs (Rbohs). Previous studies have highlighted their versatile roles in tackling different kind of stresses and in plant growth and development. In the current study, potential interacting partners and phosphorylation sites were predicted for Rboh proteins from two model species (10 Rbohs from Arabidopsis thaliana and 9 from Oryza sativa japonica). The present work is the first step towards in silico prediction of interacting partners and phosphorylation sites for Rboh proteins from two plant species. RESULTS In this work, an extensive range of potential partners (unique and common), leading to diverse functions were revealed from interaction networks and gene ontology classifications, where majority of AtRbohs and OsRbohs play role in stress-related activities, followed by cellular development. Further, 68 and 38 potential phosphorylation sites were identified in AtRbohs and OsRbohs, respectively. Their distribution, location and kinase specificities were also predicted and correlated with experimental data as well as verified with the other EF-hand containing proteins within both genomes. CONCLUSIONS Analysis of regulatory mechanisms including interaction with diverse partners and post-translational modifications like phosphorylation have provided insights regarding functional multiplicity of Rbohs. The bioinformatics-based workflow in the current study can be used to get insights for interacting partners and phosphorylation sites from Rbohs of other plant species.
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Affiliation(s)
- Gurpreet Kaur
- Department of Biotechnology, Guru Nanak Dev University (GNDU), Amritsar, Punjab, 143005, India
- Present Address: Quantitative Biology Center (QBiC), University of Tuebingen, 72076, Tuebingen, Germany
| | - Pratap Kumar Pati
- Department of Biotechnology, Guru Nanak Dev University (GNDU), Amritsar, Punjab, 143005, India.
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34
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Strandberg E, Grau-Campistany A, Wadhwani P, Bürck J, Rabanal F, Ulrich AS. Helix Fraying and Lipid-Dependent Structure of a Short Amphipathic Membrane-Bound Peptide Revealed by Solid-State NMR. J Phys Chem B 2018; 122:6236-6250. [DOI: 10.1021/acs.jpcb.8b02661] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Erik Strandberg
- Karlsruhe Institute of Technology (KIT), Institute of Biological Interfaces (IBG-2), P.O. Box 3640, 76021 Karlsruhe, Germany
| | - Ariadna Grau-Campistany
- Secció de Química Orgànica, Departament de Química Inorgànica i Orgànica, Facultat de Química, Universitat de Barcelona, 08028 Barcelona, Spain
| | - Parvesh Wadhwani
- Karlsruhe Institute of Technology (KIT), Institute of Biological Interfaces (IBG-2), P.O. Box 3640, 76021 Karlsruhe, Germany
| | - Jochen Bürck
- Karlsruhe Institute of Technology (KIT), Institute of Biological Interfaces (IBG-2), P.O. Box 3640, 76021 Karlsruhe, Germany
| | - Francesc Rabanal
- Secció de Química Orgànica, Departament de Química Inorgànica i Orgànica, Facultat de Química, Universitat de Barcelona, 08028 Barcelona, Spain
| | - Anne S. Ulrich
- Karlsruhe Institute of Technology (KIT), Institute of Biological Interfaces (IBG-2), P.O. Box 3640, 76021 Karlsruhe, Germany
- KIT, Institute of Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
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35
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Vila-Viçosa D, Silva TFD, Slaybaugh G, Reshetnyak YK, Andreev OA, Machuqueiro M. Membrane-Induced p K a Shifts in wt-pHLIP and Its L16H Variant. J Chem Theory Comput 2018; 14:3289-3297. [PMID: 29733633 DOI: 10.1021/acs.jctc.8b00102] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The pH (low) insertion peptides (pHLIPs) is a family of peptides that are able to insert into a lipid bilayer at acidic pH. The molecular mechanism of pHLIPs insertion, folding, and stability in the membrane at low pH is based on multiple protonation events, which are challenging to study at the molecular level. More specifically, the relation between the experimental p K of insertion (p Kexp) of pHLIPs and the p Ka of the key residues is yet to be clarified. We carried out a computational study, complemented with new experimental data, and established the influence of (de)protonation of titrable residues on the stability of the peptide membrane-inserted state. Constant-pH molecular dynamics simulations were employed to calculate the p Ka values of these residues along the membrane normal. In the wt-pHLIP, we identified Asp14 as the key residue for the stability of the membrane-inserted state, and its p Ka value is strongly correlated with the experimental p Kexp measured in thermodynamics studies. Also, in order to narrow down the pH range at which pHLIP is stable in the membrane, we designed a new pHLIP variant, L16H, where Leu in the 16th position was replaced by a titrable His residue. Our results showed that the L16H variant undergoes two transitions. The calculated p Ka and experimentally observed p Kexp values are in good agreement. Two distinct p Kexp values delimit a pH range where the L16H peptide is stably inserted in the membrane, while, outside this range, the membrane-inserted state is destabilized and the peptide exits from the bilayer. pHLIP peptides have been successfully used to target cancer cells for the delivery of diagnostics and therapeutic agents to acidic tumors. The fine-tuning of the stability of the pHLIP inserted state and its restriction to a narrow well-defined pH range might allow the design of new peptides, able to discriminate between tissues with different extracellular pH values.
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Affiliation(s)
- Diogo Vila-Viçosa
- Centro de Química e Bioquímica, BioISI: Biosystems and Integrative Sciences Institute, Departamento de Química e Bioquímica, Faculdade de Ciências , Universidade de Lisboa , 1749-016 Lisboa , Portugal
| | - Tomás F D Silva
- Centro de Química e Bioquímica, BioISI: Biosystems and Integrative Sciences Institute, Departamento de Química e Bioquímica, Faculdade de Ciências , Universidade de Lisboa , 1749-016 Lisboa , Portugal
| | - Gregory Slaybaugh
- Department of Physics , University of Rhode Island , 2 Lippitt Road , Kingston , Rhode Island 02881 , United States
| | - Yana K Reshetnyak
- Department of Physics , University of Rhode Island , 2 Lippitt Road , Kingston , Rhode Island 02881 , United States
| | - Oleg A Andreev
- Department of Physics , University of Rhode Island , 2 Lippitt Road , Kingston , Rhode Island 02881 , United States
| | - Miguel Machuqueiro
- Centro de Química e Bioquímica, BioISI: Biosystems and Integrative Sciences Institute, Departamento de Química e Bioquímica, Faculdade de Ciências , Universidade de Lisboa , 1749-016 Lisboa , Portugal
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36
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McGeachy AC, Caudill ER, Liang D, Cui Q, Pedersen JA, Geiger FM. Counting charges on membrane-bound peptides. Chem Sci 2018; 9:4285-4298. [PMID: 29780560 PMCID: PMC5944241 DOI: 10.1039/c8sc00804c] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Accepted: 04/02/2018] [Indexed: 01/27/2023] Open
Abstract
Quantifying the number of charges on peptides bound to interfaces requires reliable estimates of (i) surface coverage and (ii) surface charge, both of which are notoriously difficult parameters to obtain, especially at solid/water interfaces. Here, we report the thermodynamics and electrostatics governing the interactions of l-lysine and l-arginine octamers (Lys8 and Arg8) with supported lipid bilayers prepared.
Quantifying the number of charges on peptides bound to interfaces requires reliable estimates of (i) surface coverage and (ii) surface charge, both of which are notoriously difficult parameters to obtain, especially at solid/water interfaces. Here, we report the thermodynamics and electrostatics governing the interactions of l-lysine and l-arginine octamers (Lys8 and Arg8) with supported lipid bilayers prepared from a 9 : 1 mixture of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and 1,2-dimyristoyl-sn-glycero-3-phospho-(1′-rac-glycerol) (sodium salt) (DMPG) from second harmonic generation (SHG) spectroscopy, quartz crystal microbalance with dissipation monitoring (QCM-D) and nanoplasmonic sensing (NPS) mass measurements, and atomistic simulations. The combined SHG/QCM-D/NPS approach provides interfacial charge density estimates from mean field theory for the attached peptides that are smaller by a factor of approximately two (0.12 ± 0.03 C m–2 for Lys8 and 0.10 ± 0.02 C m–2 for Arg8) relative to poly-l-lysine and poly-l-arginine. These results, along with atomistic simulations, indicate that the surface charge density of the supported lipid bilayer is neutralized by the attached cationic peptides. Moreover, the number of charges associated with each attached peptide is commensurate with those found in solution; that is, Lys8 and Arg8 are fully ionized when attached to the bilayer. Computer simulations indicate Lys8 is more likely than Arg8 to “stand-up” on the surface, interacting with lipid headgroups through one or two sidechains while Arg8 is more likely to assume a “buried” conformation, interacting with the bilayer through up to six sidechains. Analysis of electrostatic potential and charge distribution from atomistic simulations suggests that the Gouy–Chapman model, which is widely used for mapping surface potential to surface charge, is semi-quantitatively valid; despite considerable orientational preference of interfacial water, the apparent dielectric constant for the interfacial solvent is about 30, due to the thermal fluctuation of the lipid–water interface.
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Affiliation(s)
- Alicia C McGeachy
- Department of Chemistry , Northwestern University , 2145 Sheridan Road , Evanston , IL 60660 , USA .
| | - Emily R Caudill
- Department of Chemistry , University of Wisconsin-Madison , 1101 University Avenue , Madison , WI 53706 , USA
| | - Dongyue Liang
- Department of Chemistry , University of Wisconsin-Madison , 1101 University Avenue , Madison , WI 53706 , USA
| | - Qiang Cui
- Department of Chemistry , University of Wisconsin-Madison , 1101 University Avenue , Madison , WI 53706 , USA.,Department of Chemistry , Boston University , 590 Commonwealth Ave. , Boston , MA 02215 , USA
| | - Joel A Pedersen
- Department of Chemistry , University of Wisconsin-Madison , 1101 University Avenue , Madison , WI 53706 , USA.,Environmental Chemistry and Technology Program , University of Wisconsin-Madison , 660 North Park Street , Madison , WI 53706 , USA.,Department of Soil Science , University of Wisconsin-Madison , 1525 Observatory Drive , Madison , WI 53706 , USA.,Department of Civil & Environmental Engineering , University of Wisconsin-Madison , 1415 Engineering Drive , Madison , WI 53706 , USA
| | - Franz M Geiger
- Department of Chemistry , Northwestern University , 2145 Sheridan Road , Evanston , IL 60660 , USA .
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37
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Zhang J, Yang W, Tan J, Ye S. In situ examination of a charged amino acid-induced structural change in lipid bilayers by sum frequency generation vibrational spectroscopy. Phys Chem Chem Phys 2018; 20:5657-5665. [PMID: 29412195 DOI: 10.1039/c7cp07389e] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The interactions between amino acids (AAs) and membranes represent various short-range and long-range interactions for biological phenomena; however, they are still poorly understood. In this study, we used cationic lysine and arginine as AA models, and systematically investigated the interactions between charged AAs and lipid bilayers using sum frequency generation vibrational spectroscopy (SFG-VS) in situ and in real time. The AA-induced dynamic structural changes of the lipid bilayer were experimentally monitored using the spectral features of CD2, CD3, the lipid head phosphate, and carbonyl groups in real time. Time-dependent SFG changes in the structure of the lipid bilayer provide direct evidence for the different interactions of lysine and arginine with the membrane. It was found that the discrepancy between lysine and arginine in binding with the lipid bilayer is due to the nature of the terminal functional groups. Arginine exhibits a more drastic impact on the membrane than lysine. SFG responses of the acyl chains, phosphate groups, and carbonyl groups provide evidence that the interaction between AAs and the membrane most likely follows an electrostatics and hydrogen bond-induced defect model. This work presents an exemplary method for comprehensive investigations of interactions between membranes and other functionally significant substances.
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Affiliation(s)
- Jiahui Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale, and Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, China.
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38
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McKay MJ, Afrose F, Koeppe RE, Greathouse DV. Helix formation and stability in membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:2108-2117. [PMID: 29447916 DOI: 10.1016/j.bbamem.2018.02.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 02/06/2018] [Accepted: 02/07/2018] [Indexed: 01/05/2023]
Abstract
In this article we review current understanding of basic principles for the folding of membrane proteins, focusing on the more abundant alpha-helical class. Membrane proteins, vital to many biological functions and implicated in numerous diseases, fold into their active conformations in the complex environment of the cell bilayer membrane. While many membrane proteins rely on the translocon and chaperone proteins to fold correctly, others can achieve their functional form in the absence of any translation apparatus or other aides. Nevertheless, the spontaneous folding process is not well understood at the molecular level. Recent findings suggest that helix fraying and loop formation may be important for overall structure, dynamics and regulation of function. Several types of membrane helices with ionizable amino acids change their topology with pH. Additionally we note that some peptides, including many that are rich in arginine, and a particular analogue of gramicidin, are able passively to translocate across cell membranes. The findings indicate that a final protein structure in a lipid-bilayer membrane is sequence-based, with lipids contributing to stability and regulation. While much progress has been made toward understanding the folding process for alpha-helical membrane proteins, it remains a work in progress. This article is part of a Special Issue entitled: Emergence of Complex Behavior in Biomembranes edited by Marjorie Longo.
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Affiliation(s)
- Matthew J McKay
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Fahmida Afrose
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Roger E Koeppe
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Denise V Greathouse
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA.
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39
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Hills RD. Refining amino acid hydrophobicity for dynamics simulation of membrane proteins. PeerJ 2018; 6:e4230. [PMID: 29340240 PMCID: PMC5767086 DOI: 10.7717/peerj.4230] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 12/14/2017] [Indexed: 11/20/2022] Open
Abstract
Coarse-grained (CG) models have been successful in simulating the chemical properties of lipid bilayers, but accurate treatment of membrane proteins and lipid-protein molecular interactions remains a challenge. The CgProt force field, original developed with the multiscale coarse graining method, is assessed by comparing the potentials of mean force for sidechain insertion in a DOPC bilayer to results reported for atomistic molecular dynamics simulations. Reassignment of select CG sidechain sites from the apolar to polar site type was found to improve the attractive interfacial behavior of tyrosine, phenylalanine and asparagine as well as charged lysine and arginine residues. The solvation energy at membrane depths of 0, 1.3 and 1.7 nm correlates with experimental partition coefficients in aqueous mixtures of cyclohexane, octanol and POPC, respectively, for sidechain analogs and Wimley-White peptides. These experimental values serve as important anchor points in choosing between alternate CG models based on their observed permeation profiles, particularly for Arg, Lys and Gln residues where the all-atom OPLS solvation energy does not agree well with experiment. Available partitioning data was also used to reparameterize the representation of the peptide backbone, which needed to be made less attractive for the bilayer hydrophobic core region. The newly developed force field, CgProt 2.4, correctly predicts the global energy minimum in the potentials of mean force for insertion of the uncharged membrane-associated peptides LS3 and WALP23. CgProt will find application in studies of lipid-protein interactions and the conformational properties of diverse membrane protein systems.
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Affiliation(s)
- Ronald D Hills
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New England, Portland, ME, United States of America
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40
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Bonhenry D, Dehez F, Tarek M. Effects of hydration on the protonation state of a lysine analog crossing a phospholipid bilayer – insights from molecular dynamics and free-energy calculations. Phys Chem Chem Phys 2018; 20:9101-9107. [DOI: 10.1039/c8cp00312b] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Protonation states of amino acids crossing lipid bilayers from multidimensional free energy surfaces.
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Affiliation(s)
| | | | - Mounir Tarek
- Université de Lorraine
- CNRS
- LPCT
- F-54000 Nancy
- France
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41
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Duan Y, Liu Y, Shen W, Zhong W. Fluorescamine Labeling for Assessment of Protein Conformational Change and Binding Affinity in Protein-Nanoparticle Interaction. Anal Chem 2017; 89:12160-12167. [PMID: 29083159 PMCID: PMC6055931 DOI: 10.1021/acs.analchem.7b02810] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Protein adsorption alters the "biological identity" of nanoparticles (NPs) and could affect how biosystems respond to invading NPs. Study of protein-NP interaction can help understand how the physicochemical properties of NPs impact the interaction and thus potentially guide the design of safer and more effective NPs for biomedical or other applications. Binding affinity between proteins and NPs and the occurrence of protein conformational change upon binding to NPs are two important aspects to be learned, but few methods are currently available to assess both simultaneously in a simple way. Herein, we demonstrated that the fluorescamine labeling method developed by our group not only could reveal protein conformational change upon adsorption to NPs, owing to its capability to label the primary amines exposed on protein surface, but also could be applied to measure the binding affinity. By screening the interaction between a large number of proteins and four types of NPs, the present study also revealed that protein adsorption onto NPs could be strongly affected by structure flexibility. The proteins with high structure flexibility experienced high degrees of conformation change when binding to the polystyrene NPs, which could potentially influence protein function. Overall, we demonstrate that our assay is a quick, simple, and high-throughput tool to reveal potential impacts on protein activity and evaluate the strength of protein-NP binding.
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Affiliation(s)
- Yaokai Duan
- Department of Chemistry, University of California, Riverside, CA USA 92521
| | - Yang Liu
- Department of Chemistry, University of California, Riverside, CA USA 92521
| | - Wen Shen
- Department of Chemistry, University of California, Riverside, CA USA 92521
| | - Wenwan Zhong
- Department of Chemistry, University of California, Riverside, CA USA 92521
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42
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Jafari M, Mehrnejad F, Doustdar F. Insight into the interactions, residue snorkeling, and membrane disordering potency of a single antimicrobial peptide into different lipid bilayers. PLoS One 2017; 12:e0187216. [PMID: 29125878 PMCID: PMC5695277 DOI: 10.1371/journal.pone.0187216] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 10/16/2017] [Indexed: 12/30/2022] Open
Abstract
Pardaxin, with a bend-helix-bend-helix structure, is a membrane-active antimicrobial peptide that its membrane activity depends on the lipid bilayer composition. Herein, all-atom molecular dynamics (MD) simulations were performed to provide further molecular insight into the interactions, structural dynamics, orientation behavior, and cationic residues snorkeling of pardaxin in the DMPC, DPPC, POPC, POPG, POPG/POPE (3:1), and POPG/POPE (1:3) lipid bilayers. The results showed that the C-terminal helix of the peptide was maintained in all six types of the model-bilayers and pardaxin was tilted into the DMPC, DPPC, and POPG/POPE mixed bilayers more than the POPC and POPG bilayers. As well as, the structure of zwitterionic membranes was more affected by the peptide than the anionic bilayers. Taken together, the study demonstrated that the cationic residues of pardaxin snorkeled toward the interface of lipid bilayers and all phenylalanine residues of the peptide played important roles in the peptide-membrane interactions. We hope that this work will provide a better understanding of the interactions of antimicrobial peptides with the membranes.
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Affiliation(s)
- Majid Jafari
- Department of Life Sciences Engineering, Faculty of New Sciences & Technologies, University of Tehran, Tehran, Iran
| | - Faramarz Mehrnejad
- Department of Life Sciences Engineering, Faculty of New Sciences & Technologies, University of Tehran, Tehran, Iran
| | - Farahnoosh Doustdar
- Department of Microbiology, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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43
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Banyikwa A, Miller SE, Krebs RA, Xiao Y, Carney JM, Braiman MS. Anhydrous Monoalkylguanidines in Aprotic and Nonpolar Solvents: Models for Deprotonated Arginine Side Chains in Membrane Environments. ACS OMEGA 2017; 2:7239-7252. [PMID: 31457300 PMCID: PMC6645140 DOI: 10.1021/acsomega.7b00281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 08/22/2017] [Indexed: 06/10/2023]
Abstract
In this study, the synthesis of crystalline dodecylguanidine free base and its spectroscopic characterization in nonpolar environments are described. IR as well as 1H and 15N NMR spectra of the free base dissolved in aprotic solvents are substantially different from the previously reported spectra of arginine, or other monoalkylguanidinium compounds, at high hydroxide concentrations. The current results provide improved modeling for the spectroscopic signals that would be expected from a deprotonated arginine in a nonpolar environment. On the basis of our spectra of the authentic dodecylguanidine free base, addition of large amounts of aqueous hydroxide to arginine or other monoalklyguanidinium salts does not deprotonate them. Instead, hydroxide addition leads to the formation of a guanidinium hydroxide complex, with a dissociation constant near ∼500 mM that accounts for the established arginine pK value of ∼13.7. We also report a method for synthesizing a compound containing both phenol and free-base guanidine groups, linked by a dodecyl chain that should be generalizable to other hydrocarbon linkers. Such alkyl-guanidine and phenolyl-alkyl-guanidine compounds can serve as small-molecule models for the conserved arginine-tyrosine groupings that have been observed in crystallographic structures of both microbial rhodopsins and G-protein-coupled receptors.
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44
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A membrane-inserted structural model of the yeast mitofusin Fzo1. Sci Rep 2017; 7:10217. [PMID: 28860650 PMCID: PMC5578988 DOI: 10.1038/s41598-017-10687-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 08/14/2017] [Indexed: 01/23/2023] Open
Abstract
Mitofusins are large transmembrane GTPases of the dynamin-related protein family, and are required for the tethering and fusion of mitochondrial outer membranes. Their full-length structures remain unknown, which is a limiting factor in the study of outer membrane fusion. We investigated the structure and dynamics of the yeast mitofusin Fzo1 through a hybrid computational and experimental approach, combining molecular modelling and all-atom molecular dynamics simulations in a lipid bilayer with site-directed mutagenesis and in vivo functional assays. The predicted architecture of Fzo1 improves upon the current domain annotation, with a precise description of the helical spans linked by flexible hinges, which are likely of functional significance. In vivo site-directed mutagenesis validates salient aspects of this model, notably, the long-distance contacts and residues participating in hinges. GDP is predicted to interact with Fzo1 through the G1 and G4 motifs of the GTPase domain. The model reveals structural determinants critical for protein function, including regions that may be involved in GTPase domain-dependent rearrangements.
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45
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Li J, Koh JJ, Liu S, Lakshminarayanan R, Verma CS, Beuerman RW. Membrane Active Antimicrobial Peptides: Translating Mechanistic Insights to Design. Front Neurosci 2017; 11:73. [PMID: 28261050 PMCID: PMC5306396 DOI: 10.3389/fnins.2017.00073] [Citation(s) in RCA: 328] [Impact Index Per Article: 46.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 01/31/2017] [Indexed: 01/10/2023] Open
Abstract
Antimicrobial peptides (AMPs) are promising next generation antibiotics that hold great potential for combating bacterial resistance. AMPs can be both bacteriostatic and bactericidal, induce rapid killing and display a lower propensity to develop resistance than do conventional antibiotics. Despite significant progress in the past 30 years, no peptide antibiotic has reached the clinic yet. Poor understanding of the action mechanisms and lack of rational design principles have been the two major obstacles that have slowed progress. Technological developments are now enabling multidisciplinary approaches including molecular dynamics simulations combined with biophysics and microbiology toward providing valuable insights into the interactions of AMPs with membranes at atomic level. This has led to increasingly robust models of the mechanisms of action of AMPs and has begun to contribute meaningfully toward the discovery of new AMPs. This review discusses the detailed action mechanisms that have been put forward, with detailed atomistic insights into how the AMPs interact with bacterial membranes. The review further discusses how this knowledge is exploited toward developing design principles for novel AMPs. Finally, the current status, associated challenges, and future directions for the development of AMP therapeutics are discussed.
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Affiliation(s)
- Jianguo Li
- Ocular Chemistry and Anti-Infectives, Singapore Eye Research InstituteSingapore, Singapore
- Agency for Science, Technology and Research (ASTAR), Bioinformatics InstituteSingapore, Singapore
- Duke-NUS Graduate Medical School, SRP Neuroscience and BDSingapore, Singapore
| | - Jun-Jie Koh
- Ocular Chemistry and Anti-Infectives, Singapore Eye Research InstituteSingapore, Singapore
| | - Shouping Liu
- Ocular Chemistry and Anti-Infectives, Singapore Eye Research InstituteSingapore, Singapore
| | | | - Chandra S. Verma
- Ocular Chemistry and Anti-Infectives, Singapore Eye Research InstituteSingapore, Singapore
- Agency for Science, Technology and Research (ASTAR), Bioinformatics InstituteSingapore, Singapore
- Department of Biological Sciences, National University of SingaporeSingapore, Singapore
- School of Biological Sciences, Nanyang Technological UniversitySingapore, Singapore
| | - Roger W. Beuerman
- Ocular Chemistry and Anti-Infectives, Singapore Eye Research InstituteSingapore, Singapore
- Duke-NUS Graduate Medical School, SRP Neuroscience and BDSingapore, Singapore
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46
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Koroloff SN, Tesch DM, Awosanya EO, Nevzorov AA. Sensitivity enhancement for membrane proteins reconstituted in parallel and perpendicular oriented bicelles obtained by using repetitive cross-polarization and membrane-incorporated free radicals. JOURNAL OF BIOMOLECULAR NMR 2017; 67:135-144. [PMID: 28205016 DOI: 10.1007/s10858-017-0090-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 01/19/2017] [Indexed: 06/06/2023]
Abstract
Multidimensional separated local-field and spin-exchange experiments employed by oriented-sample solid-state NMR are essential for structure determination and spectroscopic assignment of membrane proteins reconstituted in macroscopically aligned lipid bilayers. However, these experiments typically require a large number of scans in order to establish interspin correlations. Here we have shown that a combination of optimized repetitive cross polarization (REP-CP) and membrane-embedded free radicals allows one to enhance the signal-to-noise ratio by factors 2.4-3.0 in the case of Pf1 coat protein reconstituted in magnetically aligned bicelles with their normals being either parallel or perpendicular to the main magnetic field. Notably, spectral resolution is not affected at the 2:1 radical-to-protein ratio. Spectroscopic assignment of Pf1 coat protein in the parallel bicelles has been established as an illustration of the method. The proposed methodology will advance applications of oriented-sample NMR technique when applied to samples containing smaller quantities of proteins and three-dimensional experiments.
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Affiliation(s)
- Sophie N Koroloff
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, NC, 27695-8204, USA
| | - Deanna M Tesch
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, NC, 27695-8204, USA
- Shaw University, 118 E. South Street, Raleigh, NC, 27601, USA
| | - Emmanuel O Awosanya
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, NC, 27695-8204, USA
| | - Alexander A Nevzorov
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, NC, 27695-8204, USA.
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47
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Rajagopalan V, Greathouse DV, Koeppe RE. Influence of glutamic acid residues and pH on the properties of transmembrane helices. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:484-492. [PMID: 28069412 DOI: 10.1016/j.bbamem.2017.01.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 12/13/2016] [Accepted: 01/04/2017] [Indexed: 11/13/2022]
Abstract
Negatively charged side chains are important for the function of particular ion channels and certain other membrane proteins. To investigate the influence of single glutamic acid side chains on helices that span lipid-bilayer membranes, we have employed GWALP23 (acetyl-GGALW5LALALALALALALW19LAGA-amide) as a favorable host peptide framework. We substituted individual Leu residues with Glu residues (L12E or L14E or L16E) and incorporated specific 2H-labeled alanine residues within the core helical region or near the ends of the sequence. Solid-state 2H NMR spectra reveal little change for the core labels in GWALP23-E12, -E14 and -E16 over a pH range of 4 to 12.5, with the spectra being broader for samples in DOPC compared to DLPC bilayers. The spectra for samples with deuterium labels near the helix ends on alanines 3 and 21 show modest pH-dependent changes in the extent of unwinding of the helix terminals in DLPC and DOPC bilayers. The combined results indicate minor overall responses of these transmembrane helices to changes in pH, with the most buried residue E12 showing no pH dependence. While the Glu residues E14 and E16 may have high pKa values in the lipid bilayer environment, it is also possible that a paucity of helix response is masking the pKa values. Interestingly, when E16 is present, spectral changes at high pH report significant local unwinding of the core helix. Our results are consistent with the expectation that buried carboxyl groups aggressively hold their protons and/or waters of hydration.
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Affiliation(s)
- Venkatesan Rajagopalan
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, United States
| | - Denise V Greathouse
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, United States
| | - Roger E Koeppe
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, United States.
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48
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Fosso-Tande J, Black C, G. Aller S, Lu L, D. Hills Jr R. Simulation of lipid-protein interactions with the CgProt force field. AIMS MOLECULAR SCIENCE 2017. [DOI: 10.3934/molsci.2017.3.352] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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49
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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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50
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Panahi A, Bandara A, Pantelopulos GA, Dominguez L, Straub JE. Specific Binding of Cholesterol to C99 Domain of Amyloid Precursor Protein Depends Critically on Charge State of Protein. J Phys Chem Lett 2016; 7:3535-41. [PMID: 27525349 PMCID: PMC5293176 DOI: 10.1021/acs.jpclett.6b01624] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Recent NMR chemical shift measurements of the 99 residue C-terminal fragment of amyloid precursor protein (APP-C99) in the presence of cholesterol provide evidence of binary complex formation between C99 and cholesterol in membrane mimetic environments. It has also been observed that the production of Aβ protein is enhanced under conditions of high cholesterol concentration. In this study, we investigated the impact of the charge state of C99 on the structure and stability of the C99-cholesterol complex. We observed that the binding of C99 to cholesterol depends critically on the charge state of Glu 693 (E22) and Asp 694 (D23). Evaluation of the pKa values of the Asp and Glu side chains suggests that these residues may be predominantly neutral in existing experimental observations of a stable C99-cholesterol complex at lower pH (characteristic of the endosomal environment), while binding is destabilized near neutral pH (characteristic of the cytoplasm). These observations suggest that specific binding of cholesterol to C99 is a sensitive function of the pH encountered in vivo, with key E22 and D23 residues serving as a "pH switch" controlling C99-cholesterol binding.
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Affiliation(s)
- Afra Panahi
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts, 02215
| | - Asanga Bandara
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts, 02215
| | - George A. Pantelopulos
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts, 02215
| | - Laura Dominguez
- Biophysical Chemistry Laboratory, Physical Chemistry Department, School of Chemistry, National Autonomous University of Mexico, Mexico City, Mexico
| | - John E. Straub
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts, 02215
- Corresponding Author:
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