1
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Scott HL, Burns-Casamayor V, Dixson AC, Standaert RF, Stanley CB, Stingaciu LR, Carrillo JMY, Sumpter BG, Katsaras J, Qiang W, Heberle FA, Mertz B, Ashkar R, Barrera FN. Neutron spin echo shows pHLIP is capable of retarding membrane thickness fluctuations. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184349. [PMID: 38815687 DOI: 10.1016/j.bbamem.2024.184349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 04/03/2024] [Accepted: 05/21/2024] [Indexed: 06/01/2024]
Abstract
Cell membranes are responsible for a range of biological processes that require interactions between lipids and proteins. While the effects of lipids on proteins are becoming better understood, our knowledge of how protein conformational changes influence membrane dynamics remains rudimentary. Here, we performed experiments and computer simulations to study the dynamic response of a lipid membrane to changes in the conformational state of pH-low insertion peptide (pHLIP), which transitions from a surface-associated (SA) state at neutral or basic pH to a transmembrane (TM) α-helix under acidic conditions. Our results show that TM-pHLIP significantly slows down membrane thickness fluctuations due to an increase in effective membrane viscosity. Our findings suggest a possible membrane regulatory mechanism, where the TM helix affects lipid chain conformations, and subsequently alters membrane fluctuations and viscosity.
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Affiliation(s)
- Haden L Scott
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville 37996, United States of America
| | - Violeta Burns-Casamayor
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV 26506, United States of America
| | - Andrew C Dixson
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville 37996, United States of America
| | - Robert F Standaert
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville 37996, United States of America; C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV 26506, United States of America; Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States of America
| | - Christopher B Stanley
- Shull Wollan Center - a Joint Institute for Neutron Sciences, Oak Ridge, TN 37831, United States of America; Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States of America
| | - Laura-Roxana Stingaciu
- Labs and Soft Matter Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States of America; JCNS1, FZJ outstation at SNS, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States of America
| | - Jan-Michael Y Carrillo
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States of America; Center for Nanophase Materials Sciences, Oak Ridge, TN 37831, United States of America
| | - Bobby G Sumpter
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States of America; Center for Nanophase Materials Sciences, Oak Ridge, TN 37831, United States of America
| | - John Katsaras
- Shull Wollan Center - a Joint Institute for Neutron Sciences, Oak Ridge, TN 37831, United States of America; Labs and Soft Matter Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States of America; Department of Physics and Astronomy, University of Tennessee, Knoxville, TN 37996, United States of America
| | - Wei Qiang
- Department of Chemistry, the State University of New York, Binghamton, NY 13902, United States of America
| | - Frederick A Heberle
- Department of Chemistry, University of Tennessee, Knoxville, TN 37920, United States of America
| | - Blake Mertz
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV 26506, United States of America; West Virginia University Cancer Institute, Morgantown, WV 26506, United States of America
| | - Rana Ashkar
- Department of Physics, Virginia Tech, Blacksburg, VA 24061, United States of America; Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, VA 24061, United States of America.
| | - Francisco N Barrera
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville 37996, United States of America.
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2
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Hou M, Liu S. Recent Progress of pH-Responsive Peptides, Polypeptides, and Their Supramolecular Assemblies for Biomedical Applications. Biomacromolecules 2024. [PMID: 39105715 DOI: 10.1021/acs.biomac.4c00688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/07/2024]
Abstract
Peptides and polypeptides feature a variety of active functional groups on their side chains (including carboxylic acid, hydroxyl, amino, and thiol groups), enabling diverse chemical modifications. This versatility makes them highly valuable in stimuli-responsive systems. Notably, pH-responsive peptides and polypeptides, due to their ability to respond to pH changes, hold significant promise for applications in cellular pathology and tumor targeting. Extensive researches have highlighted the potentials of low pH insertion peptides (pHLIPs), peptide-drug conjugates (PDCs), and antibody-drug conjugates (ADCs) in biomedicine. Peptide self-assemblies, with their structural stability, ease of regulation, excellent biocompatibility, and biodegradability, offer immense potentials in the development of novel materials and biomedical applications. We also explore specific examples of their applications in drug delivery, tumor targeting, and tissue engineering, while discussing future challenges and potential advancements in the field of pH-responsive self-assembling peptide-based biomaterials.
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Affiliation(s)
- Mingxuan Hou
- Key Laboratory of Precision and Intelligent Chemistry, Department of Polymer Science and Engineering, University of Science and Technology of China, 96 Jin-zhai Road, Hefei, Anhui Province 230026, China
| | - Shiyong Liu
- Key Laboratory of Precision and Intelligent Chemistry, Department of Polymer Science and Engineering, University of Science and Technology of China, 96 Jin-zhai Road, Hefei, Anhui Province 230026, China
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3
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Greenberg ZF, Ali S, Schmittgen TD, Han S, Hughes SJ, Graim KS, He M. Peptide-based capture-and-release purification of extracellular vesicles and statistical algorithm enabled quality assessment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.06.578050. [PMID: 38370748 PMCID: PMC10871196 DOI: 10.1101/2024.02.06.578050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Circulating extracellular vesicles (EVs) have gained significant attention for discovering tumor biomarkers. However, isolating EVs with well-defined homogeneous populations from complex biological samples is challenging. Different isolation methods have been found to derive different EV populations carrying different molecular contents, which confounds current investigations and hinders subsequent clinical translation. Therefore, standardizing and building a rigorous assessment of isolated EV quality associated with downstream molecular analysis is essential. To address this need, we introduce a statistical algorithm (ExoQuality Index, EQI) by integrating multiple EV characterizations (size, particle concentration, zeta potential, total protein, and RNA), enabling direct EV quality assessment and comparisons between different isolation methods. We also introduced a novel capture-release isolation approach using a pH-responsive peptide conjugated with NanoPom magnetic beads (ExCy) for simple, fast, and homogeneous EV isolation from various biological fluids. Bioinformatic analysis of next-generation sequencing (NGS) data of EV total RNAs from pancreatic cancer patient plasma samples using our novel EV isolation approach and quality index strategy illuminates how this approach improves the identification of tumor associated molecular markers. Results showed higher human mRNA coverage compared to existing isolation approaches in terms of both pancreatic cancer pathways and EV cellular component pathways using gProfiler pathway analysis. This study provides a valuable resource for researchers, establishing a workflow to prepare and analyze EV samples carefully and contributing to the advancement of reliable and rigorous EV quality assessment and clinical translation.
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Affiliation(s)
- Zachary F. Greenberg
- Department of Pharmaceutics, College of Pharmacy, University of Florida, Gainesville, Florida 32610, United States
| | - Samantha Ali
- Department of Pharmaceutics, College of Pharmacy, University of Florida, Gainesville, Florida 32610, United States
| | - Thomas D. Schmittgen
- Department of Pharmaceutics, College of Pharmacy, University of Florida, Gainesville, Florida 32610, United States
| | - Song Han
- Department of Surgery, College of Medicine, University of Florida, Gainesville, Florida 32610, United States
| | - Steven J. Hughes
- Department of Surgery, College of Medicine, University of Florida, Gainesville, Florida 32610, United States
| | - Kiley S. Graim
- Department of Computer & Information Science & Engineering, Herbert Wertheim College of Engineering, University of Florida, Gainesville, Florida, 32610, USA
| | - Mei He
- Department of Pharmaceutics, College of Pharmacy, University of Florida, Gainesville, Florida 32610, United States
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4
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Wachira FW, Githirwa DC, McPartlon T, Nazarenko V, Gonzales JJC, Gazura MM, Leen C, Clary HR, Alston C, Klees LM, Yao L, An M. D-to-E and T19V Variants of the pH-Low Insertion Peptide and Their Doxorubicin Conjugates Interact with Membrane at Higher pH Ranges Than WT. Biochemistry 2023; 62:2997-3011. [PMID: 37793002 DOI: 10.1021/acs.biochem.3c00218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/06/2023]
Abstract
To improve targeted cargo delivery to cancer cells, pH-Low Insertion Peptide (pHLIP) variants were developed to interact with the membrane at pH values higher than those of the WT. The Asp-to-Glu variants aim to increase side chain pKa without disturbing the sequence of protonations that underpin membrane insertion. The Thr19 variants represent efforts to perturb the critical Pro20 residue. To study the effect of cargo on pHLIP insertion, doxorubicin (Dox), a fluorescent antineoplastic drug, was conjugated to selected variants near the inserting C-terminus. Variants and conjugates were characterized on a POPC membrane using Trp and Dox fluorescence methods to define the entire pH range of insertion (pHinitial-pHfinal). Compared to WT with a pHi-pHf range of 6.7-5.6, D25E-D31E-D33E, D14E-D25E-D31E-D33E, and T19V-D25E variants demonstrated higher pHi-pHf ranges of 7.3-6.1, 7.3-6.3, and 8.2-5.4, respectively. The addition of Dox expanded the pHi-pHf range, mainly by shifting pHi to higher pH values (e.g., WT pHLIP-Dox has a pHi-pHf range of 7.7-5.2). Despite the low Hill coefficient observed for the conjugates, D14E-D25E-D31E-D33E pHLIP-Dox completed insertion by a pHf of 5.7. However, the Dox cargo remained in the hydrophobic membrane interior after pHLIP insertion, which may impede drug release. Finally, a logistic function can describe pHLIP insertion as a peripheral-to-TM (start-to-finish) two-state transition; wherever possible, we discuss data deviating from such sigmoidal fitting in support of the idea that pH-specific intermediate states distinct from the initial peripheral state and the final TM state exist at intervening pH values.
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Affiliation(s)
- Faith W Wachira
- Department of Chemistry, State University of New York (SUNY), Binghamton University, Binghamton, New York 13902, United States
| | - Dancan C Githirwa
- Department of Chemistry, State University of New York (SUNY), Binghamton University, Binghamton, New York 13902, United States
| | - Thomas McPartlon
- Department of Chemistry, State University of New York (SUNY), Binghamton University, Binghamton, New York 13902, United States
| | - Vladyslav Nazarenko
- Department of Chemistry, State University of New York (SUNY), Binghamton University, Binghamton, New York 13902, United States
| | - Jerel J C Gonzales
- Department of Chemistry, State University of New York (SUNY), Binghamton University, Binghamton, New York 13902, United States
| | - Makenzie M Gazura
- Department of Chemistry, State University of New York (SUNY), Binghamton University, Binghamton, New York 13902, United States
| | - Caitlin Leen
- Department of Chemistry, State University of New York (SUNY), Binghamton University, Binghamton, New York 13902, United States
| | - Hannah R Clary
- Department of Chemistry, State University of New York (SUNY), Binghamton University, Binghamton, New York 13902, United States
| | - Claire Alston
- Department of Chemistry, State University of New York (SUNY), Binghamton University, Binghamton, New York 13902, United States
| | - Lukas M Klees
- Department of Chemistry, State University of New York (SUNY), Binghamton University, Binghamton, New York 13902, United States
| | - Lan Yao
- Department of Chemistry, State University of New York (SUNY), Binghamton University, Binghamton, New York 13902, United States
- Department of Physics, SUNY, Binghamton University, Binghamton, New York 13902, United States
| | - Ming An
- Department of Chemistry, State University of New York (SUNY), Binghamton University, Binghamton, New York 13902, United States
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5
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Ye Y, Morita S, Chang JJ, Buckley PM, Wilhelm KB, DiMaio D, Groves JT, Barrera FN. Allosteric inhibition of the T cell receptor by a designed membrane ligand. eLife 2023; 12:e82861. [PMID: 37796108 PMCID: PMC10554751 DOI: 10.7554/elife.82861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 09/20/2023] [Indexed: 10/06/2023] Open
Abstract
The T cell receptor (TCR) is a complex molecular machine that directs the activation of T cells, allowing the immune system to fight pathogens and cancer cells. Despite decades of investigation, the molecular mechanism of TCR activation is still controversial. One of the leading activation hypotheses is the allosteric model. This model posits that binding of pMHC at the extracellular domain triggers a dynamic change in the transmembrane (TM) domain of the TCR subunits, which leads to signaling at the cytoplasmic side. We sought to test this hypothesis by creating a TM ligand for TCR. Previously we described a method to create a soluble peptide capable of inserting into membranes and binding to the TM domain of the receptor tyrosine kinase EphA2 (Alves et al., eLife, 2018). Here, we show that the approach is generalizable to complex membrane receptors, by designing a TM ligand for TCR. We observed that the designed peptide caused a reduction of Lck phosphorylation of TCR at the CD3ζ subunit in T cells. As a result, in the presence of this peptide inhibitor of TCR (PITCR), the proximal signaling cascade downstream of TCR activation was significantly dampened. Co-localization and co-immunoprecipitation in diisobutylene maleic acid (DIBMA) native nanodiscs confirmed that PITCR was able to bind to the TCR. AlphaFold-Multimer predicted that PITCR binds to the TM region of TCR, where it interacts with the two CD3ζ subunits. Our results additionally indicate that PITCR disrupts the allosteric changes in the compactness of the TM bundle that occur upon TCR activation, lending support to the allosteric TCR activation model. The TCR inhibition achieved by PITCR might be useful to treat inflammatory and autoimmune diseases and to prevent organ transplant rejection, as in these conditions aberrant activation of TCR contributes to disease.
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Affiliation(s)
- Yujie Ye
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee at KnoxvilleKnoxvilleUnited States
| | - Shumpei Morita
- Department of Chemistry, University of California, BerkeleyBerkeleyUnited States
| | - Justin J Chang
- Department of Genetics, Yale UniversityNew HavenUnited States
| | - Patrick M Buckley
- Department of Microbial Pathogenesis, Yale UniversityNew HavenUnited States
| | - Kiera B Wilhelm
- Department of Chemistry, University of California, BerkeleyBerkeleyUnited States
| | - Daniel DiMaio
- Department of Genetics, Yale UniversityNew HavenUnited States
| | - Jay T Groves
- Department of Chemistry, University of California, BerkeleyBerkeleyUnited States
- Institute for Digital Molecular Analytics and Science, Nanyang Technological UniversitySingaporeSingapore
| | - Francisco N Barrera
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee at KnoxvilleKnoxvilleUnited States
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6
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Rybak JA, Sahoo AR, Kim S, Pyron RJ, Pitts SB, Guleryuz S, Smith AW, Buck M, Barrera FN. Allosteric inhibition of the epidermal growth factor receptor through disruption of transmembrane interactions. J Biol Chem 2023; 299:104914. [PMID: 37315787 PMCID: PMC10362150 DOI: 10.1016/j.jbc.2023.104914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 06/16/2023] Open
Abstract
The epidermal growth factor receptor (EGFR) is a receptor tyrosine kinase (RTK) commonly targeted for inhibition by anticancer therapeutics. Current therapeutics target EGFR's kinase domain or extracellular region. However, these types of inhibitors are not specific for tumors over healthy tissue and therefore cause undesirable side effects. Our lab has recently developed a new strategy to regulate RTK activity by designing a peptide that specifically binds to the transmembrane (TM) region of the RTK to allosterically modify kinase activity. These peptides are acidity-responsive, allowing them to preferentially target acidic environments like tumors. We have applied this strategy to EGFR and created the PET1 peptide. We observed that PET1 behaves as a pH-responsive peptide that modulates the configuration of the EGFR TM through a direct interaction. Our data indicated that PET1 inhibits EGFR-mediated cell migration. Finally, we investigated the mechanism of inhibition through molecular dynamics simulations, which showed that PET1 sits between the two EGFR TM helices; this molecular mechanism was additionally supported by AlphaFold-Multimer predictions. We propose that the PET1-induced disruption of native TM interactions disturbs the conformation of the kinase domain in such a way that it inhibits EGFR's ability to send migratory cell signals. This study is a proof-of-concept that acidity-responsive membrane peptide ligands can be generally applied to RTKs. In addition, PET1 constitutes a viable approach to therapeutically target the TM of EGFR.
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Affiliation(s)
- Jennifer A Rybak
- Department of Genome Sciences and Technology, University of Tennessee, Knoxville, Tennessee, USA
| | - Amita R Sahoo
- Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, Cleveland, Ohio, USA
| | - Soyeon Kim
- Department of Chemistry, University of Akron, Akron, Ohio, USA
| | - Robert J Pyron
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, USA
| | - Savannah B Pitts
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, USA
| | - Saffet Guleryuz
- Department of Medicine, University of Tennessee Graduate School of Medicine, Knoxville, Tennessee, USA
| | - Adam W Smith
- Department of Chemistry, University of Akron, Akron, Ohio, USA; Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Matthias Buck
- Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, Cleveland, Ohio, USA
| | - Francisco N Barrera
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, USA.
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7
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Liu YC, Wang ZX, Pan JY, Wang LQ, Dai XY, Wu KF, Ye XW, Xu XL. Recent Advances in Imaging Agents Anchored with pH (Low) Insertion Peptides for Cancer Theranostics. Molecules 2023; 28:molecules28052175. [PMID: 36903419 PMCID: PMC10004179 DOI: 10.3390/molecules28052175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 02/23/2023] [Accepted: 02/24/2023] [Indexed: 03/02/2023] Open
Abstract
The acidic extracellular microenvironment has become an effective target for diagnosing and treating tumors. A pH (low) insertion peptide (pHLIP) is a kind of peptide that can spontaneously fold into a transmembrane helix in an acidic microenvironment, and then insert into and cross the cell membrane for material transfer. The characteristics of the acidic tumor microenvironment provide a new method for pH-targeted molecular imaging and tumor-targeted therapy. As research has increased, the role of pHLIP as an imaging agent carrier in the field of tumor theranostics has become increasingly prominent. In this paper, we describe the current applications of pHLIP-anchored imaging agents for tumor diagnosis and treatment in terms of different molecular imaging methods, including magnetic resonance T1 imaging, magnetic resonance T2 imaging, SPECT/PET, fluorescence imaging, and photoacoustic imaging. Additionally, we discuss relevant challenges and future development prospects.
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Affiliation(s)
- Yu-Cheng Liu
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou 310015, China
| | - Zhi-Xian Wang
- First Clinical College of Traditional Chinese Medicine, Hunan University of Chinese Medicine, Changsha 410208, China
| | - Jing-Yi Pan
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou 310015, China
| | - Ling-Qi Wang
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou 310015, China
| | - Xin-Yi Dai
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou 310015, China
| | - Ke-Fei Wu
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou 310015, China
| | - Xue-Wei Ye
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou 310015, China
| | - Xiao-Ling Xu
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou 310015, China
- Correspondence:
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8
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McClintic WT, Scott HL, Moore N, Farahat M, Maxwell M, Schuman CD, Bolmatov D, Barrera FN, Katsaras J, Collier CP. Heterosynaptic plasticity in biomembrane memristors controlled by pH. MRS BULLETIN 2022; 48:13-21. [PMID: 36908998 PMCID: PMC9988737 DOI: 10.1557/s43577-022-00344-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/02/2022] [Indexed: 05/12/2023]
Abstract
Abstract In biology, heterosynaptic plasticity maintains homeostasis in synaptic inputs during associative learning and memory, and initiates long-term changes in synaptic strengths that nonspecifically modulate different synapse types. In bioinspired neuromorphic circuits, heterosynaptic plasticity may be used to extend the functionality of two-terminal, biomimetic memristors. In this article, we explore how changes in the pH of droplet interface bilayer aqueous solutions modulate the memristive responses of a lipid bilayer membrane in the pH range 4.97-7.40. Surprisingly, we did not find conclusive evidence for pH-dependent shifts in the voltage thresholds (V*) needed for alamethicin ion channel formation in the membrane. However, we did observe a clear modulation in the dynamics of pore formation with pH in time-dependent, pulsed voltage experiments. Moreover, at the same voltage, lowering the pH resulted in higher steady-state currents because of increased numbers of conductive peptide ion channels in the membrane. This was due to increased partitioning of alamethicin monomers into the membrane at pH 4.97, which is below the pKa (~5.3-5.7) of carboxylate groups on the glutamate residues of the peptide, making the monomers more hydrophobic. Neutralization of the negative charges on these residues, under acidic conditions, increased the concentration of peptide monomers in the membrane, shifting the equilibrium concentrations of peptide aggregate assemblies in the membrane to favor greater numbers of larger, increasingly more conductive pores. It also increased the relaxation time constants for pore formation and decay, and enhanced short-term facilitation and depression of the switching characteristics of the device. Modulating these thresholds globally and independently of alamethicin concentration and applied voltage will enable the assembly of neuromorphic computational circuitry with enhanced functionality. Impact statement We describe how to use pH as a modulatory "interneuron" that changes the voltage-dependent memristance of alamethicin ion channels in lipid bilayers by changing the structure and dynamical properties of the bilayer. Having the ability to independently control the threshold levels for pore conduction from voltage or ion channel concentration enables additional levels of programmability in a neuromorphic system. In this article, we note that barriers to conduction from membrane-bound ion channels can be lowered by reducing solution pH, resulting in higher currents, and enhanced short-term learning behavior in the form of paired-pulse facilitation. Tuning threshold values with environmental variables, such as pH, provide additional training and learning algorithms that can be used to elicit complex functionality within spiking neural networks. Graphical abstract Supplementary information The online version contains supplementary material available at 10.1557/s43577-022-00344-z.
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Affiliation(s)
- William T. McClintic
- Bredesen Center for Interdisciplinary Research, The University of Tennessee, Knoxville, USA
| | - Haden L. Scott
- Large Scale Structures Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, USA
| | - Nick Moore
- Department of Biochemistry & Cellular and Molecular Biology, The University of Tennessee, Knoxville, USA
| | - Mustafa Farahat
- Department of Chemical and Biomolecular Engineering, The University of Tennessee, Knoxville, USA
| | - Mikayla Maxwell
- Department of Biochemistry & Cellular and Molecular Biology, The University of Tennessee, Knoxville, USA
| | - Catherine D. Schuman
- Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, USA
| | - Dima Bolmatov
- Shull Wollan Center, Oak Ridge National Laboratory, Oak Ridge, USA
| | - Francisco N. Barrera
- Department of Biochemistry & Cellular and Molecular Biology, The University of Tennessee, Knoxville, USA
| | - John Katsaras
- Large Scale Structures Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, USA
- Shull Wollan Center, Oak Ridge National Laboratory, Oak Ridge, USA
| | - C. Patrick Collier
- Bredesen Center for Interdisciplinary Research, The University of Tennessee, Knoxville, USA
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, USA
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9
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Deskeuvre M, Lan J, Dierge E, Messens J, Riant O, Corbet C, Feron O, Frédérick R. Targeting cancer cells in acidosis with conjugates between the carnitine palmitoyltransferase 1 inhibitor etomoxir and pH (low) Insertion Peptides. Int J Pharm 2022; 624:122041. [PMID: 35868479 DOI: 10.1016/j.ijpharm.2022.122041] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 07/07/2022] [Accepted: 07/18/2022] [Indexed: 10/17/2022]
Abstract
Targeting enzymes involved in tumor metabolism is a promising way to tackle cancer progression. The inhibition of carnitine palmitoyltransferase 1 (CPT1) by etomoxir (Eto) efficiently slows down the growth of various cancers. Unfortunately, the clinical use of this drug was abandoned because of hepatotoxic effects. We report the development of pH-sensitive peptide (pHLIP)-drug conjugate to deliver Eto selectively to cancer cells exposed to acidic microenvironmental conditions. A newly designed sequence for the pHLIP peptide, named pHLIPd, was compared with a previously published reference pHLIP peptide, named pHLIPr. We showed that the conjugate between pHLIPd and Eto has a better pH-dependent insertion and structuration than the pHLIPr-based conjugate inside POPC vesicles. We observed antiproliferative effects when applied on acid-adapted cancer cells, reaching a larger inhibitory activity than Eto alone. In conclusion, this study brings the first evidence that pHLIP-based conjugates with a CPT1 inhibitor has the potential to specifically target the tumor acidic compartment and exert anticancer effects while sparing healthy tissues.
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Affiliation(s)
- Marine Deskeuvre
- Louvain Drug Research Institute (LDRI), Medicinal Chemistry Research Group (CMFA), Université Catholique de Louvain (UCLouvain), 73 Avenue Emmanuel Mounier, B-1200 Brussel, Belgium; Pole of Pharmacology and Therapeutics (FATH), Institut de Recherche Expérimentale et Clinique (IREC), Université Catholique de Louvain (UCLouvain), 57 Avenue Hippocrate B1.57.04, B-1200 Brussels, Belgium
| | - Junjie Lan
- Institute of Condensed Matter and Nanosciences, MOST Division, Place Louis Pasteur, Université Catholique de Louvain (UCLouvain), Louvain-la-Neuve B-1348, Belgium
| | - Emeline Dierge
- Pole of Pharmacology and Therapeutics (FATH), Institut de Recherche Expérimentale et Clinique (IREC), Université Catholique de Louvain (UCLouvain), 57 Avenue Hippocrate B1.57.04, B-1200 Brussels, Belgium
| | - Joris Messens
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie (VIB), 1050 Brussels, Belgium; Brussels Center for Redox Biology, 1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel (VUB), 1050 Brussels, Belgium
| | - Olivier Riant
- Institute of Condensed Matter and Nanosciences, MOST Division, Place Louis Pasteur, Université Catholique de Louvain (UCLouvain), Louvain-la-Neuve B-1348, Belgium
| | - Cyril Corbet
- Pole of Pharmacology and Therapeutics (FATH), Institut de Recherche Expérimentale et Clinique (IREC), Université Catholique de Louvain (UCLouvain), 57 Avenue Hippocrate B1.57.04, B-1200 Brussels, Belgium
| | - Olivier Feron
- Pole of Pharmacology and Therapeutics (FATH), Institut de Recherche Expérimentale et Clinique (IREC), Université Catholique de Louvain (UCLouvain), 57 Avenue Hippocrate B1.57.04, B-1200 Brussels, Belgium
| | - Raphaël Frédérick
- Louvain Drug Research Institute (LDRI), Medicinal Chemistry Research Group (CMFA), Université Catholique de Louvain (UCLouvain), 73 Avenue Emmanuel Mounier, B-1200 Brussel, Belgium.
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10
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Ataka K, Drauschke J, Stulberg V, Koksch B, Heberle J. pH-induced insertion of pHLIP into a lipid bilayer: In-situ SEIRAS characterization of a folding intermediate at neutral pH. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183873. [PMID: 35104491 DOI: 10.1016/j.bbamem.2022.183873] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 11/22/2021] [Accepted: 01/20/2022] [Indexed: 06/14/2023]
Abstract
The pH low insertion peptide (pHLIP) is a pH-sensitive cell penetrating peptide that transforms from an unstructured coil on the membrane surface at pH > 7, to a transmembrane (TM) α-helix at pH < 5. By exploiting this unique property, pHLIP attracts interest as a potential tool for drug delivery and visualisation of acidic tissues produced by various maladies such as cancer, inflammation, hypoxia etc. Even though the structures of initial and end states of pHLIP insertion have been widely accepted, the intermediate structures in between these two states are less clear. Here, we have applied in situ Surface-Enhanced Infrared Absorption spectroscopy to examine the pH-induced insertion and folding processes of pHLIP into a solid-supported lipid bilayer. We show that formation of partially helical structure already takes place at pH only slightly below 7.0, but with the helical axis parallel to the membrane surface. The peptide starts to reorientate its helix from horizontal to vertical direction, accompanied by the insertion into the TM region at pH < 6.2. Further insertion into the TM region of the peptide results in an increase of inherent α-helical structure and complete secondary structure formation at pH 5.3. Analysis of the changes of the carboxylate vibrational bands upon pH titration shows two distinctive groups of aspartates and glutamates with pKa values of 4.5 and 6.3, respectively. Comparison to the amide bands of the peptide backbone suggests that the latter Asp/Glu groups are directly involved in the conformational changes of pHLIP in the respective intermediate states.
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Affiliation(s)
- Kenichi Ataka
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany.
| | - Janina Drauschke
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Valentina Stulberg
- Institute for Chemistry and Biochemistry, Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Arnimallee 20, 14195, Berlin, Germany
| | - Beate Koksch
- Institute for Chemistry and Biochemistry, Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Arnimallee 20, 14195, Berlin, Germany
| | - Joachim Heberle
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany.
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11
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Schaefer KG, Grau B, Moore N, Mingarro I, King GM, Barrera FN. Controllable membrane remodeling by a modified fragment of the apoptotic protein Bax. Faraday Discuss 2021; 232:114-130. [PMID: 34549736 PMCID: PMC8712456 DOI: 10.1039/d0fd00070a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Intrinsic apoptosis is orchestrated by a group of proteins that mediate the coordinated disruption of mitochondrial membranes. Bax is a multi-domain protein that, upon activation, disrupts the integrity of the mitochondrial outer membrane by forming pores. We strategically introduced glutamic acids into a short sequence of the Bax protein that constitutively creates membrane pores. The resulting BaxE5 peptide efficiently permeabilizes membranes at acidic pH, showing low permeabilization at neutral pH. Atomic force microscopy (AFM) imaging showed that at acidic pH BaxE5 established several membrane remodeling modalities that progressively disturbed the integrity of the lipid bilayer. The AFM data offers vistas on the membrane disruption process, which starts with pore formation and progresses through localized exposure of membrane monolayers leading to stable and small (height ∼ 16 Å) lipid-peptide complexes. The different types of membrane morphology observed in the presence of BaxE5 suggest that the peptide can establish different types of membrane interactions. BaxE5 adopts a rare unstructured conformation when bound to membranes, which might facilitate the dynamic transition between those different states, and then promote membrane digestion.
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Affiliation(s)
- Katherine G Schaefer
- Department of Physics and Astronomy, University of Missouri, Columbia, MO 65211, USA.
| | - Brayan Grau
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, 37996, USA.
- Departament de Bioquímica i Biologia Molecular, Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI BioTecMed), Universitat de València, E-46100 Burjassot, Spain
| | - Nicolas Moore
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, 37996, USA.
| | - Ismael Mingarro
- Departament de Bioquímica i Biologia Molecular, Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI BioTecMed), Universitat de València, E-46100 Burjassot, Spain
| | - Gavin M King
- Department of Physics and Astronomy, University of Missouri, Columbia, MO 65211, USA.
- Department of Biochemistry, University of Missouri, Columbia, Missouri, 65211, USA
| | - Francisco N Barrera
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, 37996, USA.
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12
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Otieno SA, Qiang W. Roles of key residues and lipid dynamics reveal pHLIP-membrane interactions at intermediate pH. Biophys J 2021; 120:4649-4662. [PMID: 34624273 PMCID: PMC8595900 DOI: 10.1016/j.bpj.2021.10.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 09/16/2021] [Accepted: 10/01/2021] [Indexed: 11/16/2022] Open
Abstract
The pH-low insertion peptide (pHLIP) and its analogs sense the microenvironmental pH variations in tumorous cells and serve as useful anticancer drug deliveries. The pHLIP binds peripherally to membranes and adopts random coil conformation at the physiological pH. The peptide switches from random coil to α-helical conformation and inserts unidirectionally into membrane bilayers when pH drops below a critical transition value that has been routinely determined by the Trp fluorescence spectroscopy. Recent high-resolution studies using solid-state NMR spectroscopy revealed the presence of thermodynamically stable intermediate states of membrane-associated pHLIP around the fluorescence-based transition pH-value. However, the molecular structural features and their mechanistic roles of these intermediate states in the pH-driven membrane insertion process of pHLIP remain largely unknown. This work utilizes solid-state NMR spectroscopy to explore 1) the mechanistic roles of key proline and arginine residues within the pHLIP sequence at intermediate pH-values, and 2) the changes in lipid dynamics at intermediate pH-values in multiple types of model bilayers with anionic phospholipid and/or cholesterol. Our results demonstrate several molecular structural and dynamics changes at around the transition pH-values, including the isomerization of proline-threonine backbone configuration, breaking of arginine-aspartic acid salt bridge and the formation of arginine-lipid interactions, and a universal decreasing of dynamics in lipid headgroups and alkyl chains. Overall, the outcomes provide important insights on the molecular interactions between pHLIP and membrane bilayers at intermediate pH-values and, therefore, prompt the understanding of pH-driven membrane insertion process of this anticancer drug-delivering peptide.
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Affiliation(s)
- Sarah A Otieno
- Department of Chemistry, Binghamton University, State University of New York, Binghamton, New York
| | - Wei Qiang
- Department of Chemistry, Binghamton University, State University of New York, Binghamton, New York.
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13
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Westerfield JM, Sahoo AR, Alves DS, Grau B, Cameron A, Maxwell M, Schuster JA, Souza PCT, Mingarro I, Buck M, Barrera FN. Conformational Clamping by a Membrane Ligand Activates the EphA2 Receptor. J Mol Biol 2021; 433:167144. [PMID: 34229012 DOI: 10.1016/j.jmb.2021.167144] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 06/03/2021] [Accepted: 06/30/2021] [Indexed: 02/07/2023]
Abstract
The EphA2 receptor is a promising drug target for cancer treatment, since EphA2 activation can inhibit metastasis and tumor progression. It has been recently described that the TYPE7 peptide activates EphA2 using a novel mechanism that involves binding to the single transmembrane domain of the receptor. TYPE7 is a conditional transmembrane (TM) ligand, which only inserts into membranes at neutral pH in the presence of the TM region of EphA2. However, how membrane interactions can activate EphA2 is not known. We systematically altered the sequence of TYPE7 to identify the binding motif used to activate EphA2. With the resulting six peptides, we performed biophysical and cell migration assays that identified a new potent peptide variant. We also performed a mutational screen that determined the helical interface that mediates dimerization of the TM domain of EphA2 in cells. These results, together with molecular dynamic simulations, allowed to elucidate the molecular mechanism that TYPE7 uses to activate EphA2, where the membrane peptide acts as a molecular clamp that wraps around the TM dimer of the receptor. We propose that this binding mode stabilizes the active conformation of EphA2. Our data, additionally, provide clues into the properties that TM ligands need to have in order to achieve activation of membrane receptors.
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Affiliation(s)
- Justin M Westerfield
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, 1311 Cumberland Avenue, Knoxville, TN 37996, USA
| | - Amita R Sahoo
- Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - Daiane S Alves
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, 1311 Cumberland Avenue, Knoxville, TN 37996, USA
| | - Brayan Grau
- Departament de Bioquímica i Biologia Molecular, Institut Universitari de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València, E-46100 Burjassot, Spain
| | - Alayna Cameron
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, 1311 Cumberland Avenue, Knoxville, TN 37996, USA
| | - Mikayla Maxwell
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, 1311 Cumberland Avenue, Knoxville, TN 37996, USA
| | - Jennifer A Schuster
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, 1311 Cumberland Avenue, Knoxville, TN 37996, USA
| | - Paulo C T Souza
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS & University of Lyon, 7 Passage du Vercors, F-69367 Lyon, France
| | - Ismael Mingarro
- Departament de Bioquímica i Biologia Molecular, Institut Universitari de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València, E-46100 Burjassot, Spain
| | - Matthias Buck
- Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - Francisco N Barrera
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, 1311 Cumberland Avenue, Knoxville, TN 37996, USA.
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14
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Silva TFD, Vila-Viçosa D, Machuqueiro M. Improved Protocol to Tackle the pH Effects on Membrane-Inserting Peptides. J Chem Theory Comput 2021; 17:3830-3840. [PMID: 34115492 DOI: 10.1021/acs.jctc.1c00020] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Many important biological pathways rely on membrane-interacting peptides or proteins, which can alter the biophysical properties of the cell membrane by simply adsorbing to its surface to undergo a full insertion process. To study these phenomena with atomistic detail, model peptides have been used to refine the current computational methodologies. Improvements have been made with force-field parameters, enhanced sampling techniques to obtain faster sampling, and the addition of chemical-physical properties, such as pH, whose influence dramatically increases at the water/membrane interface. The pH (low) insertion peptide (pHLIP) is a peptide that inserts across a membrane bilayer depending on the pH due to the presence of a key residue (Asp14) whose acidity-induced protonation triggers the whole process. The complex nature of these peptide/membrane interactions resulted in sampling limitations of the protonation and configurational space albeit using state-of-the-art methods such as the constant-pH molecular dynamics. To address this issue and circumvent those limitations, new simulations were performed with our newly developed pH-replica exchange method using wild-type (wt)-pHLIP in different 2-oleoyl-1-palmitoyl-sn-glycero-3-phosphocholine membrane sizes. This technique provided enhanced sampling and allowed for the calculation of more complete Asp14 pKa profiles. The conformational heterogeneity derived from strong electrostatic interactions between Asp14 and the lipid phosphate groups was identified as the source of most pKa variability. In spite of these persistent and harder-to-equilibrate phosphate interactions, the pKa values at deeper regions (6.0-6.2) still predicted the experimental pK of insertion (6.0) since the electrostatic perturbation decays as the residue inserts further into the membrane. We also observed that reducing the system size leads to membrane deformations where it increasingly loses the ability to accommodate the pHLIP-induced perturbations. This indicates that large membrane patches, such as 256 or even 352 lipids, are needed to obtain stable and more realistic pHLIP/membrane systems. These results strengthen our method pKa predictive and analytical capabilities to study the intricate play of electrostatic effects of the peptide/membrane interface, granting confidence for future applications in similar systems.
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Affiliation(s)
- Tomás F D Silva
- Departamento de Química e Bioquímica, Faculdade de Ciências, BioISI: Biosystems and Integrative Sciences Institute, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Diogo Vila-Viçosa
- Departamento de Química e Bioquímica, Faculdade de Ciências, BioISI: Biosystems and Integrative Sciences Institute, Universidade de Lisboa, 1749-016 Lisboa, Portugal.,Kinetikos, Coimbra, Portugal
| | - Miguel Machuqueiro
- Departamento de Química e Bioquímica, Faculdade de Ciências, BioISI: Biosystems and Integrative Sciences Institute, Universidade de Lisboa, 1749-016 Lisboa, Portugal
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15
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Pharmacokinetic modeling reveals parameters that govern tumor targeting and delivery by a pH-Low Insertion Peptide (pHLIP). Proc Natl Acad Sci U S A 2021; 118:2016605118. [PMID: 33443162 PMCID: PMC7817199 DOI: 10.1073/pnas.2016605118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Tumors exhibit an acidic extracellular microenvironment that is accentuated at cell surfaces. As a result, they can be targeted by a pH-Low Insertion Peptide (pHLIP), an acid-triggered tumor-targeting peptide that can also serve as a vehicle for drug delivery. In this work, we use a pharmacokinetic modeling approach to deepen our understanding of the mechanisms and factors that influence pHLIP tumor targeting and delivery, and also identify factors that do not. In so doing, we predict pHLIP phenotypes with significantly enhanced capabilities. The model may therefore be useful for guiding the future development of pHLIP variants. A pH-Low Insertion Peptide (pHLIP) is a pH-sensitive peptide that undergoes membrane insertion, resulting in transmembrane helix formation, on exposure to acidity at a tumor cell surface. As a result, pHLIPs preferentially accumulate within tumors and can be used for tumor-targeted imaging and drug delivery. Here we explore the determinants of pHLIP insertion, targeting, and delivery through a computational modeling approach. We generate a simple mathematical model to describe the transmembrane insertion process and then integrate it into a pharmacokinetic model, which predicts the tumor vs. normal tissue biodistribution of the most studied pHLIP, “wild-type pHLIP,” over time after a single intravenous injection. From these models, we gain insight into the various mechanisms behind pHLIP tumor targeting and delivery, as well as the various biological parameters that influence it. Furthermore, we analyze how changing the properties of pHLIP can influence the efficacy of tumor targeting and delivery, and we predict the properties for optimal pHLIP phenotypes that have superior tumor targeting and delivery capabilities compared with wild-type pHLIP.
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16
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Burns V, Mertz B. Using Simulation to Understand the Role of Titration on the Stability of a Peptide-Lipid Bilayer Complex. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:12272-12280. [PMID: 32988206 PMCID: PMC7778881 DOI: 10.1021/acs.langmuir.0c02038] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The pH-low insertion peptide (pHLIP) is an anionic membrane-active peptide with promising potential for applications in imaging of cancer tumors and targeted delivery of chemotherapeutics. The key advantage of pHLIP lies in its acid sensitivity: in acidic cellular environments, pHLIP can insert unidirectionally into the plasma membrane. Partitioning-folding coupling is triggered by titration of the acidic residues in pHLIP, transforming pHLIP from a hydrophilic to a hydrophobic peptide. Despite this knowledge, the reverse pathway that leads to exit of the peptide from the plasma membrane is poorly understood. Our hypothesis is that sequential deprotonation of pHLIP is a prerequisite for exit of the peptide from the plasma membrane. We carried out molecular dynamics (MD) simulations to characterize the effect that deprotonation of the acidic residues of pHLIP has on the stability of the peptide when inserted into a model lipid bilayer of 1-palmitoyl-2-oleoyl-sn-3-phosphocholine (POPC). Initiation of the exit mechanism is facilitated by a complex relationship between the peptide, bulk solvent, and the membrane environment. As the N-terminal acidic residues of pHLIP are deprotonated, localized loss of helicity drives unfolding of the peptide and more pronounced interactions with the bilayer at the lipid-water interface. Deprotonation of the C-terminal acidic residues (D25, D31, D33, and E34) leads to further loss of secondary structure distal from the C-terminus, as well as formation of a water channel that stabilizes the orientation of pHLIP parallel to the membrane normal. Together, these results help explain how stabilization of intermediates between the surface-bound and inserted states of pHLIP occur and provide insights into rational design of pHLIP variants with modified abilities of insertion.
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Affiliation(s)
- Violetta Burns
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Blake Mertz
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States
- WVU Cancer Institute, West Virginia University, Morgantown, West Virginia 26506, United States
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17
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Reshetnyak YK, Moshnikova A, Andreev OA, Engelman DM. Targeting Acidic Diseased Tissues by pH-Triggered Membrane-Associated Peptide Folding. Front Bioeng Biotechnol 2020; 8:335. [PMID: 32411684 PMCID: PMC7198868 DOI: 10.3389/fbioe.2020.00335] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 03/26/2020] [Indexed: 12/19/2022] Open
Abstract
The advantages of targeted therapy have motivated many efforts to find distinguishing features between the molecular cell surface landscapes of diseased and normal cells. Typically, the features have been proteins, lipids or carbohydrates, but other approaches are emerging. In this discussion, we examine the use of cell surface acidity as a feature that can be exploited by using pH-sensitive peptide folding to target agents to diseased cell surfaces or cytoplasms.
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Affiliation(s)
- Yana K Reshetnyak
- Department of Physics, The University of Rhode Island, Kingston, RI, United States
| | - Anna Moshnikova
- Department of Physics, The University of Rhode Island, Kingston, RI, United States
| | - Oleg A Andreev
- Department of Physics, The University of Rhode Island, Kingston, RI, United States
| | - Donald M Engelman
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
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18
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Svoronos AA, Bahal R, Pereira MC, Barrera FN, Deacon JC, Bosenberg M, DiMaio D, Glazer PM, Engelman DM. Tumor-Targeted, Cytoplasmic Delivery of Large, Polar Molecules Using a pH-Low Insertion Peptide. Mol Pharm 2020; 17:461-471. [PMID: 31855437 DOI: 10.1021/acs.molpharmaceut.9b00883] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Tumor-targeted drug delivery systems offer not only the advantage of an enhanced therapeutic index, but also the possibility of overcoming the limitations that have largely restricted drug design to small, hydrophobic, "drug-like" molecules. Here, we explore the ability of a tumor-targeted delivery system centered on the use of a pH-low insertion peptide (pHLIP) to directly deliver moderately polar, multi-kDa molecules into tumor cells. A pHLIP is a short, pH-responsive peptide capable of inserting across a cell membrane to form a transmembrane helix at acidic pH. pHLIPs target the acidic tumor microenvironment with high specificity, and a drug attached to the inserting end of a pHLIP can be translocated across the cell membrane during the insertion process. We investigate the ability of wildtype pHLIP to deliver peptide nucleic acid (PNA) cargoes of varying sizes across lipid membranes. We find that pHLIP effectively delivers PNAs up to ∼7 kDa into cells in a pH-dependent manner. In addition, pHLIP retains its tumor-targeting capabilities when linked to cargoes of this size, although the amount delivered is reduced for PNA cargoes greater than ∼6 kDa. As drug-like molecules are traditionally restricted to sizes of ∼500 Da, this constitutes an order-of-magnitude expansion in the size range of deliverable drug candidates.
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Affiliation(s)
| | - Raman Bahal
- Department of Pharmaceutical Sciences , University of Connecticut , Storrs , Connecticut 06269 , United States
| | - Mohan C Pereira
- Department of Science & Mathematics , Cedarville University , Cedarville , Ohio 45314 , United States
| | - Francisco N Barrera
- Department of Biochemistry & Cellular and Molecular Biology , University of Tennessee , Knoxville , Tennessee 37996 , United States
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19
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Rao BD, Chakraborty H, Chaudhuri A, Chattopadhyay A. Differential sensitivity of pHLIP to ester and ether lipids. Chem Phys Lipids 2019; 226:104849. [PMID: 31836521 DOI: 10.1016/j.chemphyslip.2019.104849] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 12/05/2019] [Accepted: 12/05/2019] [Indexed: 10/25/2022]
Abstract
pH (low) insertion peptide (pHLIP) is a polypeptide from the third transmembrane helix of bacteriorhodopsin. The pH-dependent membrane insertion of pHLIP has been conveniently exploited for translocation of cargo molecules and as a novel imaging agent in cancer biology due to low extracellular pH in cancer tissues. Although the application of pHLIP for imaging tumor and targeted drug delivery is well studied, literature on pHLIP-membrane interaction is relatively less studied. Keeping this in mind, we explored the differential interaction of pHLIP with ester and ether lipid membranes utilizing fluorescence and CD spectroscopy. We report, for the first time, higher binding affinity of pHLIP toward ether lipid relative to ester lipid membranes. There results gain relevance since Halobacterium halobium (source of bacteriorhodopsin) is enriched with ether lipids. In addition, we monitored the difference in microenvironment around pHLIP tryptophans utilizing red edge excitation shift and observed increased motional restriction of water molecules in the interfacial region in ether lipid membranes. These changes were accompanied with increase in helicity of pHLIP in ether lipid relative to ester lipid membranes. Our results assume further relevance since ether lipids are upregulated in cancer cells and have emerged as potential biomarkers of various diseases including cancer.
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Affiliation(s)
- Bhagyashree D Rao
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500 007, India; CSIR-Indian Institute of Chemical Technology, Uppal Road, Hyderabad, 500 007, India; Academy of Scientific and Innovative Research, Ghaziabad, 201 002, India
| | - Hirak Chakraborty
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500 007, India; School of Chemistry, Sambalpur University, Jyoti Vihar, Burla, Odisha, 768 019, India
| | - Arunima Chaudhuri
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500 007, India
| | - Amitabha Chattopadhyay
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500 007, India; Academy of Scientific and Innovative Research, Ghaziabad, 201 002, India.
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20
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Nguyen MHL, DiPasquale M, Rickeard BW, Doktorova M, Heberle FA, Scott HL, Barrera FN, Taylor G, Collier CP, Stanley CB, Katsaras J, Marquardt D. Peptide-Induced Lipid Flip-Flop in Asymmetric Liposomes Measured by Small Angle Neutron Scattering. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:11735-11744. [PMID: 31408345 PMCID: PMC7393738 DOI: 10.1021/acs.langmuir.9b01625] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Despite the prevalence of lipid transbilayer asymmetry in natural plasma membranes, most biomimetic model membranes studied are symmetric. Recent advances have helped to overcome the difficulties in preparing asymmetric liposomes in vitro, allowing for the examination of a larger set of relevant biophysical questions. Here, we investigate the stability of asymmetric bilayers by measuring lipid flip-flop with time-resolved small-angle neutron scattering (SANS). Asymmetric large unilamellar vesicles with inner bilayer leaflets containing predominantly 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and outer leaflets composed mainly of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) displayed slow spontaneous flip-flop at 37 ◦C (half-time, t1/2 = 140 h). However, inclusion of peptides, namely, gramicidin, alamethicin, melittin, or pHLIP (i.e., pH-low insertion peptide), accelerated lipid flip-flop. For three of these peptides (i.e., pHLIP, alamethicin, and melittin), each of which was added externally to preformed asymmetric vesicles, we observed a completely scrambled bilayer in less than 2 h. Gramicidin, on the other hand, was preincorporated during the formation of the asymmetric liposomes and showed a time resolvable 8-fold increase in the rate of lipid asymmetry loss. These results point to a membrane surface-related (e.g., adsorption/insertion) event as the primary driver of lipid scrambling in the asymmetric model membranes of this study. We discuss the implications of membrane peptide binding, conformation, and insertion on lipid asymmetry.
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Affiliation(s)
- Michael H. L. Nguyen
- Department of Chemistry and Biochemistry, University
of Windsor, Windsor, N9B 3P4 ON Canada
| | - Mitchell DiPasquale
- Department of Chemistry and Biochemistry, University
of Windsor, Windsor, N9B 3P4 ON Canada
| | - Brett W. Rickeard
- Department of Chemistry and Biochemistry, University
of Windsor, Windsor, N9B 3P4 ON Canada
| | - Milka Doktorova
- Department of Integrative Biology and Pharmacology,
University of Texas Health Science Center at Houston, Houston, Texas 77225, United
States
| | - Frederick A. Heberle
- Department of Integrative Biology and Pharmacology,
University of Texas Health Science Center at Houston, Houston, Texas 77225, United
States
- Center for Environmental Biotechnology, University
of Tennessee, Knoxville, Tennessee 37996, United States
| | - Haden L. Scott
- Center for Environmental Biotechnology, University
of Tennessee, Knoxville, Tennessee 37996, United States
- Department of Biochemistry & Cellular and
Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United
States
| | - Francisco N. Barrera
- Department of Biochemistry & Cellular and
Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United
States
| | - Graham Taylor
- The Bredesen Center, University of Tennessee,
Knoxville, Tennessee 37996, United States
| | - Charles P. Collier
- The Bredesen Center, University of Tennessee,
Knoxville, Tennessee 37996, United States
- Center for Nanophase Materials Sciences, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Christopher B. Stanley
- Neutron Scattering Division, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37831, United States
| | - John Katsaras
- Large Scale Structures Group, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37831, United States
- Shull Wollan Center, a Joint Institute for Neutron
Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United
States
- Department of Physics and Astronomy, University of
Tennessee, Knoxville, Tennessee 37996, United States
| | - Drew Marquardt
- Department of Chemistry and Biochemistry, University
of Windsor, Windsor, N9B 3P4 ON Canada
- Department of Physics, University of Windsor, Windsor, N9B
3P4 ON Canada
- Corresponding Author:
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21
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Schlebach JP. Ions at the Interface: Pushing the pK of pHLIP. Biophys J 2019; 117:793-794. [PMID: 31400915 DOI: 10.1016/j.bpj.2019.07.035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 07/24/2019] [Indexed: 10/26/2022] Open
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22
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Nguyen VP, Dixson AC, Barrera FN. The Effect of Phosphatidylserine on a pH-Responsive Peptide Is Defined by Its Noninserting End. Biophys J 2019; 117:659-667. [PMID: 31400916 PMCID: PMC6712489 DOI: 10.1016/j.bpj.2019.07.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 06/26/2019] [Accepted: 07/15/2019] [Indexed: 02/08/2023] Open
Abstract
The acidity-triggered rational membrane (ATRAM) peptide was designed to target acidic diseases such as cancer. An acidic extracellular medium, such as that found in aggressive tumors, drives the protonation of the glutamic acids in ATRAM, leading to the membrane translocation of its C-terminus and the formation of a transmembrane helix. Compared to healthy cells, cancerous cells often increase exposure of the negatively charged phosphatidylserine (PS) on the outer leaflet of the plasma membrane. Here we use a reconstituted vesicle system to explore how PS influences the interaction of ATRAM with membranes. To explore this, we used two new variants of ATRAM, termed K2-ATRAM and Y-ATRAM, with small modifications at the noninserting N-terminus. We observed that the effect of PS on the membrane insertion pK and lipid partitioning hinged on the sequence of the noninserting end. Our data additionally indicate that the effect of PS on the insertion pK does not merely depend on electrostatics, but it is multifactorial. Here we show how small sequence changes can impact the interaction of a peptide with membranes of mixed lipid composition. These data illustrate how model studies using neutral bilayers, which do not mimic the negative charge found in the plasma membrane of cancer cells, may fail to capture important aspects of the interaction of anticancer peptides with tumor cells. This information can guide the design of therapeutic peptides that target the acidic environments of different diseased tissues.
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Affiliation(s)
- Vanessa P Nguyen
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee
| | - Andrew C Dixson
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee
| | - Francisco N Barrera
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee.
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23
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Westerfield J, Gupta C, Scott HL, Ye Y, Cameron A, Mertz B, Barrera FN. Ions Modulate Key Interactions between pHLIP and Lipid Membranes. Biophys J 2019; 117:920-929. [PMID: 31422821 DOI: 10.1016/j.bpj.2019.07.034] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 07/05/2019] [Accepted: 07/22/2019] [Indexed: 02/04/2023] Open
Abstract
The pH-low insertion peptide (pHLIP) is used for targeted delivery of drug cargoes to acidic tissues such as tumors. The extracellular acidosis found in solid tumors triggers pHLIP to transition from a membrane-adsorbed state to fold into a transmembrane α-helix. Different factors influence the acidity required for pHLIP to insert into lipid membranes. One of them is the lipid headgroup composition, which defines the electrostatic profile of the membrane. However, the molecular interactions that drive the adsorption of pHLIP to the bilayer surface are poorly understood. In this study, we combine biophysical experiments and all-atom molecular dynamics simulations to understand the role played by electrostatics in the interaction between pHLIP and a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine bilayer. We observed that the solution ionic strength affects the structure of pHLIP at the membrane surface as well as the acidity needed for different steps in the membrane insertion process. In particular, our simulations revealed that an increase in ionic strength affected both pHLIP and the bilayer; the coordination of sodium ions with the C-terminus of pHLIP led to localized changes in helicity, whereas the coordination of sodium ions with the phosphate moiety of the phosphocholine headgroups had a condensing effect on our model bilayer. These results are relevant to our understanding of environmental influences on the ability of pHLIP to adsorb to the cell membrane and are useful in our fundamental understanding of the absorption of pH-responsive peptides and cell-penetrating peptides.
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Affiliation(s)
- Justin Westerfield
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee-Knoxville, Knoxville, Tennessee
| | - Chitrak Gupta
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia
| | - Haden L Scott
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee-Knoxville, Knoxville, Tennessee
| | - Yujie Ye
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee-Knoxville, Knoxville, Tennessee
| | - Alayna Cameron
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee-Knoxville, Knoxville, Tennessee
| | - Blake Mertz
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia; WVU Cancer Institute, West Virginia University, Morgantown, West Virginia.
| | - Francisco N Barrera
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee-Knoxville, Knoxville, Tennessee.
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24
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Nguyen VP, Palanikumar L, Kennel SJ, Alves DS, Ye Y, Wall JS, Magzoub M, Barrera FN. Mechanistic insights into the pH-dependent membrane peptide ATRAM. J Control Release 2019; 298:142-153. [PMID: 30763623 PMCID: PMC6408977 DOI: 10.1016/j.jconrel.2019.02.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 01/28/2019] [Accepted: 02/08/2019] [Indexed: 12/12/2022]
Abstract
pH-responsive peptides are promising therapeutic molecules that can specifically target the plasma membrane in the acidified extracellular medium that bathes cells in tumors. We designed the acidity-triggered rational membrane (ATRAM) peptide to have a pH-responsive membrane interaction. At physiological pH, ATRAM binds to the membrane surface in a largely unstructured conformation, while in acidic conditions it inserts into lipid bilayers forming a transmembrane helix. However, the molecular mechanism ATRAM uses to target and insert into tumor cells remains poorly understood. Here, we determined that ATRAM inserts into cancer cells with a preferential membrane orientation, where the C-terminus of the peptide traverses the plasma membrane and explores the cytoplasm. Using biophysical techniques, we determined that the membrane interaction of ATRAM is contingent on the concentration of the peptide. Kinetic studies showed that membrane insertion occurs in at least three steps, where only the first step was affected by the membrane density of ATRAM. These observations, combined with membrane binding and leakage data, indicate that the interaction of ATRAM with lipid membranes is dependent on its oligomerization state. SPECT/CT imaging in mice revealed that ATRAM accumulates in the blood pool, where it has a prolonged circulation time (> 4 h). Since fast peptide clearance and degradation in circulation are major problems for clinical development, we studied the mechanism ATRAM uses to remain in the blood stream. Using binding and transfer assays, we determined that ATRAM binds reversibly to human serum albumin. We propose that ATRAM uses albumin as a carrier in the blood stream to evade clearance and proteolysis before interacting with the plasma membrane of cancer cells. We also show that ATRAM is able to be deliver liposomes to cells in a pH dependent way. Our data highlight the potential of ATRAM as a specific therapeutic agent for diseases that lead to acidic tissues, including cancer.
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Affiliation(s)
- Vanessa P Nguyen
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, United States
| | - Loganathan Palanikumar
- Biology Program, Division of Science, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Stephen J Kennel
- Departments of Medicine & Radiology, University of Tennessee Medical Center, Knoxville, TN, United States
| | - Daiane S Alves
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, United States
| | - Yujie Ye
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, United States
| | - Jonathan S Wall
- Departments of Medicine & Radiology, University of Tennessee Medical Center, Knoxville, TN, United States
| | - Mazin Magzoub
- Biology Program, Division of Science, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Francisco N Barrera
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, United States.
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25
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Scott HL, Heberle FA, Katsaras J, Barrera FN. Phosphatidylserine Asymmetry Promotes the Membrane Insertion of a Transmembrane Helix. Biophys J 2019; 116:1495-1506. [PMID: 30954213 DOI: 10.1016/j.bpj.2019.03.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 02/13/2019] [Accepted: 03/06/2019] [Indexed: 11/18/2022] Open
Abstract
The plasma membrane (PM) contains an asymmetric distribution of lipids between the inner and outer bilayer leaflets. A lipid of special interest in eukaryotic membranes is the negatively charged phosphatidylserine (PS). In healthy cells, PS is actively sequestered to the inner leaflet of the PM, but PS redistributes to the outer leaflet when the cell is damaged or at the onset of apoptosis. However, the influence of PS asymmetry on membrane protein structure and folding are poorly understood. The pH low insertion peptide (pHLIP) adsorbs to the membrane surface at a neutral pH, but it inserts into the membrane at an acidic pH. We have previously observed that in symmetric vesicles, PS affects the membrane insertion of pHLIP by lowering the pH midpoint of insertion. Here, we studied the effect of PS asymmetry on the membrane interaction of pHLIP. We developed a modified protocol to create asymmetric vesicles containing PS and employed Annexin V labeled with an Alexa Fluor 568 fluorophore as a new probe to quantify PS asymmetry. We observed that the membrane insertion of pHLIP was promoted by the asymmetric distribution of negatively charged PS, which causes a surface charge difference between bilayer leaflets. Our results indicate that lipid asymmetry can modulate the formation of an α-helix on the membrane. A corollary is that model studies using symmetric bilayers to mimic the PM may fail to capture important aspects of protein-membrane interactions.
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Affiliation(s)
- Haden L Scott
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee
| | - Frederick A Heberle
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee; Shull Wollan Center-a Joint Institute for Neutron Sciences, Oak Ridge, Tennessee
| | - John Katsaras
- Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee; Shull Wollan Center-a Joint Institute for Neutron Sciences, Oak Ridge, Tennessee; Large Scale Structures Group, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee; Department of Physics, Brock University, St. Catharines, Ontario, Canada
| | - Francisco N Barrera
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee.
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26
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Salassi S, Canepa E, Ferrando R, Rossi G. Anionic nanoparticle-lipid membrane interactions: the protonation of anionic ligands at the membrane surface reduces membrane disruption. RSC Adv 2019; 9:13992-13997. [PMID: 35519336 PMCID: PMC9064125 DOI: 10.1039/c9ra02462j] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 04/25/2019] [Indexed: 11/21/2022] Open
Abstract
Monolayer-protected gold nanoparticles (Au NPs) are promising biomedical tools with applications in diagnosis and therapy, thanks to their biocompatibility and versatility. Here we show how the NP surface functionalization can drive the mechanism of interaction with lipid membranes. In particular, we show that the spontaneous protonation of anionic carboxylic groups on the NP surface can make the NP-membrane interaction faster and less disruptive. The interaction between anionic Au nanoparticles and model lipid membranes is facilitated by the spontaneous protonation of the NP ligand carboxylate groups, COO−˙ → COOH, in the lipid headgroup region.![]()
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Affiliation(s)
| | - Ester Canepa
- Department of Chemistry and Industrial Chemistry
- University of Genoa
- 16146 Genoa
- Italy
| | | | - Giulia Rossi
- Department of Physics
- University of Genoa
- 16146 Genoa
- Italy
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27
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pH-dependent thermodynamic intermediates of pHLIP membrane insertion determined by solid-state NMR spectroscopy. Proc Natl Acad Sci U S A 2018; 115:12194-12199. [PMID: 30442664 DOI: 10.1073/pnas.1809190115] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The applications of the pH low insertion peptide (pHLIP) in cancer diagnosis and cross-membrane cargo delivery have drawn increasing attention in the past decade. With its origin as the transmembrane (TM) helix C of bacteriorhodopsin, pHLIP is also an important model for understanding how pH can affect the folding and topogenesis of a TM α-helix. Protonations of multiple D/E residues transform pHLIP from an unstructured coil at membrane surface (known as state II, at pH ≥ 7) to a TM α-helix (state III, pH ≤ 5.3). While these initial and end states of pHLIP insertion have been firmly established, what happens at the intervening pH values is less clear. However, the intervening pH range is most relevant to pHLIP-cell interactions in the acidic extracellular tumor environment (and in the endosomes within cells). Here, using advanced solid-state NMR spectroscopy with palmitoyl-2-oleoyl-sn-glycerol-3-phosphocholine unilamellar vesicles as the model membrane, we systematically examined the state of pHLIP-membrane interactions (in terms of the membrane locations of D/E residues, as well as lipid dynamics) at the intervening pH values of 6.4, 6.1, and 5.8, along with the known states at pH 7.4 and 5.3. Thermodynamic intermediate states distinct from the initial and end states were discovered to exist at each of the intervening pH examined. They support a multistage model of pHLIP insertion in which the D/E titrations occur in a defined sequence at distinct intermediate pH values. This multistage model has important ramifications in pHLIP applications.
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28
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Gupta C, Ren Y, Mertz B. Cooperative Nonbonded Forces Control Membrane Binding of the pH-Low Insertion Peptide pHLIP. Biophys J 2018; 115:2403-2412. [PMID: 30503536 DOI: 10.1016/j.bpj.2018.11.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 10/10/2018] [Accepted: 11/01/2018] [Indexed: 02/06/2023] Open
Abstract
Peptides with the ability to bind and insert into the cell membrane have immense potential in biomedical applications. pH (low) insertion peptide (pHLIP), a water-soluble polypeptide derived from helix C of bacteriorhodopsin, can insert into a membrane at acidic pH to form a stable transmembrane α-helix. The insertion process takes place in three stages: pHLIP is unstructured and soluble in water at neutral pH (state I), unstructured and bound to the surface of a membrane at neutral pH (state II), and inserted into the membrane as an α-helix at low pH (state III). Using molecular dynamics simulations, we have modeled state II of pHLIP and a fast-folding variant of pHLIP, in which each peptide is bound to a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine bilayer surface. Our results provide strong support for recently published spectroscopic studies, namely that pHLIP preferentially binds to the bilayer surface as a function of location of anionic amino acids and that backbone dehydration occurs upon binding. Unexpectedly, we also observed several instances of segments of pHLIP folding into a stable helical turn. Our results provide a molecular level of detail that is essential to providing new insights into pHLIP function and to facilitate design of variants with improved membrane-active capabilities.
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Affiliation(s)
- Chitrak Gupta
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia
| | - Yue Ren
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia
| | - Blake Mertz
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia.
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29
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Alves DS, Westerfield JM, Shi X, Nguyen VP, Stefanski KM, Booth KR, Kim S, Morrell-Falvey J, Wang BC, Abel SM, Smith AW, Barrera FN. A novel pH-dependent membrane peptide that binds to EphA2 and inhibits cell migration. eLife 2018; 7:36645. [PMID: 30222105 PMCID: PMC6192698 DOI: 10.7554/elife.36645] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 09/16/2018] [Indexed: 12/19/2022] Open
Abstract
Misregulation of the signaling axis formed by the receptor tyrosine kinase (RTK) EphA2 and its ligand, ephrinA1, causes aberrant cell-cell contacts that contribute to metastasis. Solid tumors are characterized by an acidic extracellular medium. We intend to take advantage of this tumor feature to design new molecules that specifically target tumors. We created a novel pH-dependent transmembrane peptide, TYPE7, by altering the sequence of the transmembrane domain of EphA2. TYPE7 is highly soluble and interacts with the surface of lipid membranes at neutral pH, while acidity triggers transmembrane insertion. TYPE7 binds to endogenous EphA2 and reduces Akt phosphorylation and cell migration as effectively as ephrinA1. Interestingly, we found large differences in juxtamembrane tyrosine phosphorylation and the extent of EphA2 clustering when comparing TYPE7 with activation by ephrinA1. This work shows that it is possible to design new pH-triggered membrane peptides to activate RTK and gain insights on its activation mechanism.
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Affiliation(s)
- Daiane S Alves
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, United States
| | - Justin M Westerfield
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, United States
| | - Xiaojun Shi
- Department of Chemistry, University of Akron, Akron, United States.,Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, United States.,Pharmacology, Case Western Reserve University, Cleveland, United States.,Rammelkamp Center for Research, MetroHealth Medical Center, Cleveland, United States
| | - Vanessa P Nguyen
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, United States
| | - Katherine M Stefanski
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, United States
| | - Kristen R Booth
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, United States
| | - Soyeon Kim
- Department of Chemistry, University of Akron, Akron, United States
| | - Jennifer Morrell-Falvey
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, United States.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, United States
| | - Bing-Cheng Wang
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, United States.,Pharmacology, Case Western Reserve University, Cleveland, United States.,Rammelkamp Center for Research, MetroHealth Medical Center, Cleveland, United States
| | - Steven M Abel
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, United States.,National Institute for Mathematical and Biological Synthesis, University of Tennessee, Knoxville, United States
| | - Adam W Smith
- Department of Chemistry, University of Akron, Akron, United States
| | - Francisco N Barrera
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, United States
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30
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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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31
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Vasquez-Montes V, Gerhart J, King KE, Thévenin D, Ladokhin AS. Comparison of lipid-dependent bilayer insertion of pHLIP and its P20G variant. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1860:534-543. [PMID: 29138065 DOI: 10.1016/j.bbamem.2017.11.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 10/18/2017] [Accepted: 11/10/2017] [Indexed: 02/07/2023]
Abstract
The ability of the pH-Low Insertion Peptide (pHLIP) to insert into lipid membranes in a transbilayer conformation makes it an important tool for targeting acidic diseased tissues. pHLIP can also serve as a model template for thermodynamic studies of membrane insertion. We use intrinsic fluorescence and circular dichroism spectroscopy to examine the effect of replacing pHLIP's central proline on the pH-triggered lipid-dependent conformational switching of the peptide. We find that the P20G variant (pHLIP-P20G) has a higher helical propensity than the native pHLIP (pHLIP-WT), in both water:organic solvent mixtures and in the presence of lipid bilayers. Spectral shifts of tryptophan fluorescence reveal that with both pHLIP-WT and pHLIP-P20G, the deeply penetrating interfacial form (traditionally called State II) is populated only in pure phosphocholine bilayers. The presence of either anionic lipids or phosphatidylethanolamine leads to a much shallower penetration of the peptide (referred to here as State IIS, for "shallow"). This novel state can be differentiated from soluble state by a reduction in accessibility of tryptophans to acrylamide and by FRET to vesicles doped with Dansyl-PE, but not by a spectral shift in fluorescence emission. FRET experiments indicate free energies for interfacial partitioning range from 6.2 to 6.8kcal/mol and are marginally more favorable for pHLIP-P20G. The effective pKa for the insertion of both peptides depends on the lipid composition, but is always higher for pHLIP-P20G than for pHLIP-WT by approximately one pH unit, which corresponds to a difference of 1.3kcal/mol in free energy of protonation favoring insertion of pHLIP-P20G.
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Affiliation(s)
- Victor Vasquez-Montes
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, 66160, United States
| | - Janessa Gerhart
- Department of Chemistry, Lehigh University, Bethlehem, PA, 18015, United States
| | - Kelly E King
- Department of Chemistry, Lehigh University, Bethlehem, PA, 18015, United States
| | - Damien Thévenin
- Department of Chemistry, Lehigh University, Bethlehem, PA, 18015, United States
| | - Alexey S Ladokhin
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, 66160, United States.
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