1
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Miller B, Kim SJ, Cao K, Mehta HH, Thumaty N, Kumagai H, Iida T, McGill C, Pike CJ, Nurmakova K, Levine ZA, Sullivan PM, Yen K, Ertekin-Taner N, Atzmon G, Barzilai N, Cohen P. Humanin variant P3S is associated with longevity in APOE4 carriers and resists APOE4-induced brain pathology. Aging Cell 2024:e14153. [PMID: 38520065 DOI: 10.1111/acel.14153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 03/07/2024] [Accepted: 03/10/2024] [Indexed: 03/25/2024] Open
Abstract
The APOE4 allele is recognized as a significant genetic risk factor to Alzheimer's disease (AD) and influences longevity. Nonetheless, some APOE4 carriers exhibit resistance to AD even in advanced age. Humanin, a mitochondrial-derived peptide comprising 24 amino acids, has variants linked to cognitive resilience and longevity. Our research uncovered a unique humanin variant, P3S, specifically enriched in centenarians with the APOE4 allele. Through in silico analyses and subsequent experimental validation, we demonstrated a strong affinity between humanin P3S and APOE4. Utilizing an APOE4-centric mouse model of amyloidosis (APP/PS1/APOE4), we observed that humanin P3S significantly attenuated brain amyloid-beta accumulation compared to the wild-type humanin. Transcriptomic assessments of mice treated with humanin P3S highlighted its potential mechanism involving the enhancement of amyloid beta phagocytosis. Additionally, in vitro studies corroborated humanin P3S's efficacy in promoting amyloid-beta clearance. Notably, in the temporal cortex of APOE4 carriers, humanin expression is correlated with genes associated with phagocytosis. Our findings suggest a role of the rare humanin variant P3S, especially prevalent among individuals of Ashkenazi descent, in mitigating amyloid beta pathology and facilitating phagocytosis in APOE4-linked amyloidosis, underscoring its significance in longevity and cognitive health among APOE4 carriers.
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Affiliation(s)
- Brendan Miller
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, California, USA
| | - Su-Jeong Kim
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, California, USA
| | - Kevin Cao
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, California, USA
| | - Hemal H Mehta
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, California, USA
| | - Neehar Thumaty
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, California, USA
| | - Hiroshi Kumagai
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, California, USA
| | - Tomomitsu Iida
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, California, USA
| | - Cassandra McGill
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, California, USA
| | - Christian J Pike
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, California, USA
| | - Kamila Nurmakova
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Zachary A Levine
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Patrick M Sullivan
- Department of Medicine (Geriatrics), Duke University Medical Center, Durham, North Carolina, USA
| | - Kelvin Yen
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, California, USA
| | | | - Gil Atzmon
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Biology, Faculty of Natural Sciences, University of Haifa, Haifa, Israel
| | - Nir Barzilai
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Pinchas Cohen
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, California, USA
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2
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Steinsaltz M, Levine ZA. Assessing p53 aggregates over a lifetime: Studies on young, adult, and aged mice. Biophys J 2023; 122:351a. [PMID: 36783783 DOI: 10.1016/j.bpj.2022.11.1947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
Affiliation(s)
- Matthew Steinsaltz
- Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
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3
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Abstract
Improving adhesives for wet surfaces is an ongoing challenge. While the adhesive proteins of marine mussels have inspired many synthetic wet adhesives, the mechanisms of mussel adhesion are still not fully understood. Using surface forces apparatus (SFA) measurements and replica-exchange and umbrella-sampling molecular dynamics simulations, we probed the relationships between the sequence, structure, and adhesion of mussel-inspired peptides. Experimental and computational results reveal that peptides derived from mussel foot protein 3 slow (mfp-3s) containing 3,4-dihydroxyphenylalanine (Dopa), a post-translationally modified variant of tyrosine commonly found in mussel foot proteins, form adhesive monolayers on mica. In contrast, peptides with tyrosine adsorb as weakly adhesive clusters. We further considered simulations of mfp-3s derivatives on a range of hydrophobic and hydrophilic organic and inorganic surfaces (including silica, self-assembled monolayers, and a lipid bilayer) and demonstrated that the chemical character of the target surface and proximity of cationic and hydrophobic residues to Dopa affect peptide adsorption and adhesion. Collectively, our results suggest that conversion of tyrosine to Dopa in hydrophobic, sparsely charged peptides influences peptide self-association and ultimately dictates their adhesive performance.
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Affiliation(s)
- George D Degen
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, California 93106, United States
| | - Keila C Cunha
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93106, United States
| | - Zachary A Levine
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut 06510, United States.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06510, United States
| | - J Herbert Waite
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93106, United States.,Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, California 93106, United States.,Marine Science Institute, University of California, Santa Barbara, Santa Barbara, California 93106, United States
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93106, United States.,Department of Physics, University of California, Santa Barbara, Santa Barbara, California 93106, United States
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4
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Miazek A, Zalas M, Skrzymowska J, Bogin BA, Grzymajło K, Goszczynski TM, Levine ZA, Morrow JS, Stankewich MC. Age-dependent ataxia and neurodegeneration caused by an αII spectrin mutation with impaired regulation of its calpain sensitivity. Sci Rep 2021; 11:7312. [PMID: 33790315 PMCID: PMC8012654 DOI: 10.1038/s41598-021-86470-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 03/15/2021] [Indexed: 12/15/2022] Open
Abstract
The neuronal membrane-associated periodic spectrin skeleton (MPS) contributes to neuronal development, remodeling, and organization. Post-translational modifications impinge on spectrin, the major component of the MPS, but their role remains poorly understood. One modification targeting spectrin is cleavage by calpains, a family of calcium-activated proteases. Spectrin cleavage is regulated by activated calpain, but also by the calcium-dependent binding of calmodulin (CaM) to spectrin. The physiologic significance of this balance between calpain activation and substrate-level regulation of spectrin cleavage is unknown. We report a strain of C57BL/6J mice harboring a single αII spectrin point mutation (Sptan1 c.3293G > A:p.R1098Q) with reduced CaM affinity and intrinsically enhanced sensitivity to calpain proteolysis. Homozygotes are embryonic lethal. Newborn heterozygotes of either gender appear normal, but soon develop a progressive ataxia characterized biochemically by accelerated calpain-mediated spectrin cleavage and morphologically by disruption of axonal and dendritic integrity and global neurodegeneration. Molecular modeling predicts unconstrained exposure of the mutant spectrin's calpain-cleavage site. These results reveal the critical importance of substrate-level regulation of spectrin cleavage for the maintenance of neuronal integrity. Given that excessive activation of calpain proteases is a common feature of neurodegenerative disease and traumatic encephalopathy, we propose that damage to the spectrin MPS may contribute to the neuropathology of many disorders.
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Affiliation(s)
- Arkadiusz Miazek
- Department of Tumor Immunology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Weigla 12, 53-114, Wrocław, Poland
- Department of Biochemistry and Molecular Biology, Wroclaw University of Environmental and Life Sciences, Norwida 31, 50-375, Wrocław, Poland
| | - Michał Zalas
- Department of Tumor Immunology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Weigla 12, 53-114, Wrocław, Poland
| | - Joanna Skrzymowska
- Department of Tumor Immunology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Weigla 12, 53-114, Wrocław, Poland
| | - Bryan A Bogin
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Krzysztof Grzymajło
- Department of Biochemistry and Molecular Biology, Wroclaw University of Environmental and Life Sciences, Norwida 31, 50-375, Wrocław, Poland
| | - Tomasz M Goszczynski
- Department of Tumor Immunology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Weigla 12, 53-114, Wrocław, Poland
| | - Zachary A Levine
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Department of Pathology, Yale University School of Medicine, 310 Cedar Street, LH108, New Haven, CT, 06520, USA
| | - Jon S Morrow
- Department of Pathology, Yale University School of Medicine, 310 Cedar Street, LH108, New Haven, CT, 06520, USA.
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, USA.
| | - Michael C Stankewich
- Department of Pathology, Yale University School of Medicine, 310 Cedar Street, LH108, New Haven, CT, 06520, USA.
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Gray ALH, Antevska A, Link BA, Bogin B, Burke SJ, Dupuy SD, Collier JJ, Levine ZA, Karlstad MD, Do TD. α-CGRP disrupts amylin fibrillization and regulates insulin secretion: implications on diabetes and migraine. Chem Sci 2021; 12:5853-5864. [PMID: 34168810 PMCID: PMC8179678 DOI: 10.1039/d1sc01167g] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 03/13/2021] [Indexed: 11/21/2022] Open
Abstract
Despite being relatively benign and not an indicative signature of toxicity, fibril formation and fibrillar structures continue to be key factors in assessing the structure-function relationship in protein aggregation diseases. The inability to capture molecular cross-talk among key players at the tissue level before fibril formation greatly accounts for the missing link toward the development of an efficacious therapeutic intervention for Type II diabetes mellitus (T2DM). We show that human α-calcitonin gene-related peptide (α-CGRP) remodeled amylin fibrillization. Furthermore, while CGRP and/or amylin monomers reduce the secretion of both mouse Ins1 and Ins2 proteins, CGRP oligomers have a reverse effect on Ins1. Genetically reduced Ins2, the orthologous version of human insulin, has been shown to enhance insulin sensitivity and extend the life-span in old female mice. Beyond the mechanistic insights, our data suggest that CGRP regulates insulin secretion and lowers the risk of T2DM. Our result rationalizes how migraine might be protective against T2DM. We envision the new paradigm of CGRP : amylin interactions as a pivotal aspect for T2DM diagnostics and therapeutics. Maintaining a low level of amylin while increasing the level of CGRP could become a viable approach toward T2DM prevention and treatment.
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Affiliation(s)
- Amber L H Gray
- Department of Chemistry, University of Tennessee Knoxville TN 37996 USA
| | | | - Benjamin A Link
- Department of Chemistry, University of Tennessee Knoxville TN 37996 USA
| | - Bryan Bogin
- Department of Pathology, Yale School of Medicine New Haven CT 06520 USA
- Department of Molecular Biophysics & Biochemistry, Yale University New Haven CT 0652 USA
| | - Susan J Burke
- Laboratory of Immunogenetics, Pennington Biomedical Research Center Baton Rouge LA 70808 USA
| | - Samuel D Dupuy
- Department of Surgery, Graduate School of Medicine, University of Tennessee Health Science Center Knoxville TN 37920 USA
| | - J Jason Collier
- Laboratory of Islet Biology and Inflammation, Pennington Biomedical Research Center Baton Rouge LA 70808 USA
| | - Zachary A Levine
- Department of Pathology, Yale School of Medicine New Haven CT 06520 USA
- Department of Molecular Biophysics & Biochemistry, Yale University New Haven CT 0652 USA
| | - Michael D Karlstad
- Department of Surgery, Graduate School of Medicine, University of Tennessee Health Science Center Knoxville TN 37920 USA
| | - Thanh D Do
- Department of Chemistry, University of Tennessee Knoxville TN 37996 USA
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6
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Abstract
The loss of proteostasis over the life course is associated with a wide range of debilitating degenerative diseases and is a central hallmark of human aging. When left unchecked, proteins that are intrinsically disordered can pathologically aggregate into highly ordered fibrils, plaques, and tangles (termed amyloids), which are associated with countless disorders such as Alzheimer's disease, Parkinson's disease, type II diabetes, cancer, and even certain viral infections. However, despite significant advances in protein folding and solution biophysics techniques, determining the molecular cause of these conditions in humans has remained elusive. This has been due, in part, to recent discoveries showing that soluble protein oligomers, not insoluble fibrils or plaques, drive the majority of pathological processes. This has subsequently led researchers to focus instead on heterogeneous and often promiscuous protein oligomers. Unfortunately, significant gaps remain in how to prepare, model, experimentally corroborate, and extract amyloid oligomers relevant to human disease in a systematic manner. This Review will report on each of these techniques and their successes and shortcomings in an attempt to standardize comparisons between protein oligomers across disciplines, especially in the context of neurodegeneration. By standardizing multiple techniques and identifying their common overlap, a clearer picture of the soluble neuropathological aggresome can be constructed and used as a baseline for studying human disease and aging.
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Affiliation(s)
- Gregory-Neal Gomes
- Department of Pathology, Yale School of Medicine, New Haven, CT, 06520, USA
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Zachary A. Levine
- Department of Pathology, Yale School of Medicine, New Haven, CT, 06520, USA
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA
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7
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Mei Z, Treado JD, Grigas AT, Levine ZA, Regan L, O'Hern CS. Analyses of protein cores reveal fundamental differences between solution and crystal structures. Proteins 2020; 88:1154-1161. [PMID: 32105366 PMCID: PMC7415476 DOI: 10.1002/prot.25884] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 02/05/2020] [Accepted: 02/23/2020] [Indexed: 12/20/2022]
Abstract
There have been several studies suggesting that protein structures solved by NMR spectroscopy and X-ray crystallography show significant differences. To understand the origin of these differences, we assembled a database of high-quality protein structures solved by both methods. We also find significant differences between NMR and crystal structures-in the root-mean-square deviations of the C α atomic positions, identities of core amino acids, backbone, and side-chain dihedral angles, and packing fraction of core residues. In contrast to prior studies, we identify the physical basis for these differences by modeling protein cores as jammed packings of amino acid-shaped particles. We find that we can tune the jammed packing fraction by varying the degree of thermalization used to generate the packings. For an athermal protocol, we find that the average jammed packing fraction is identical to that observed in the cores of protein structures solved by X-ray crystallography. In contrast, highly thermalized packing-generation protocols yield jammed packing fractions that are even higher than those observed in NMR structures. These results indicate that thermalized systems can pack more densely than athermal systems, which suggests a physical basis for the structural differences between protein structures solved by NMR and X-ray crystallography.
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Affiliation(s)
- Zhe Mei
- Integrated Graduate Program in Physical & Engineering Biology, Yale University, New Haven, Connecticut
- Department of Chemistry, Yale University, New Haven, Connecticut
| | - John D Treado
- Integrated Graduate Program in Physical & Engineering Biology, Yale University, New Haven, Connecticut
- Department of Mechanical Engineering & Materials Science, Yale University, New Haven, Connecticut
| | - Alex T Grigas
- Integrated Graduate Program in Physical & Engineering Biology, Yale University, New Haven, Connecticut
- Graduate Program in Computational Biology & Bioinformatics, Yale University, New Haven, Connecticut
| | - Zachary A Levine
- Department of Pathology, Yale University, New Haven, Connecticut
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut
| | - Lynne Regan
- Institute of Quantitative Biology, Biochemistry and Biotechnology, Center for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Corey S O'Hern
- Integrated Graduate Program in Physical & Engineering Biology, Yale University, New Haven, Connecticut
- Department of Mechanical Engineering & Materials Science, Yale University, New Haven, Connecticut
- Department of Physics, Yale University, New Haven, Connecticut
- Department of Applied Physics, Yale University, New Haven, Connecticut
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8
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Grigas AT, Mei Z, Treado JD, Levine ZA, Regan L, O'Hern CS. Using physical features of protein core packing to distinguish real proteins from decoys. Protein Sci 2020; 29:1931-1944. [PMID: 32710566 PMCID: PMC7454528 DOI: 10.1002/pro.3914] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 07/10/2020] [Accepted: 07/20/2020] [Indexed: 01/06/2023]
Abstract
The ability to consistently distinguish real protein structures from computationally generated model decoys is not yet a solved problem. One route to distinguish real protein structures from decoys is to delineate the important physical features that specify a real protein. For example, it has long been appreciated that the hydrophobic cores of proteins contribute significantly to their stability. We used two sources to obtain datasets of decoys to compare with real protein structures: submissions to the biennial Critical Assessment of protein Structure Prediction competition, in which researchers attempt to predict the structure of a protein only knowing its amino acid sequence, and also decoys generated by 3DRobot, which have user-specified global root-mean-squared deviations from experimentally determined structures. Our analysis revealed that both sets of decoys possess cores that do not recapitulate the key features that define real protein cores. In particular, the model structures appear more densely packed (because of energetically unfavorable atomic overlaps), contain too few residues in the core, and have improper distributions of hydrophobic residues throughout the structure. Based on these observations, we developed a feed-forward neural network, which incorporates key physical features of protein cores, to predict how well a computational model recapitulates the real protein structure without knowledge of the structure of the target sequence. By identifying the important features of protein structure, our method is able to rank decoy structures with similar accuracy to that obtained by state-of-the-art methods that incorporate many additional features. The small number of physical features makes our model interpretable, emphasizing the importance of protein packing and hydrophobicity in protein structure prediction.
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Affiliation(s)
- Alex T. Grigas
- Graduate Program in Computational Biology and BioinformaticsYale UniversityNew HavenConnecticutUSA
- Integrated Graduate Program in Physical and Engineering BiologyYale UniversityNew HavenConnecticutUSA
| | - Zhe Mei
- Integrated Graduate Program in Physical and Engineering BiologyYale UniversityNew HavenConnecticutUSA
- Department of ChemistryYale UniversityNew HavenConnecticutUSA
| | - John D. Treado
- Integrated Graduate Program in Physical and Engineering BiologyYale UniversityNew HavenConnecticutUSA
- Department of Mechanical Engineering and Materials ScienceYale UniversityNew HavenConnecticutUSA
| | - Zachary A. Levine
- Department of PathologyYale UniversityNew HavenConnecticutUSA
- Department of Molecular Biophysics and BiochemistryYale UniversityNew HavenConnecticutUSA
| | - Lynne Regan
- Institute of Quantitative Biology, Biochemistry and Biotechnology, Centre for Synthetic and Systems Biology, School of Biological SciencesUniversity of EdinburghEdinburghUK
| | - Corey S. O'Hern
- Graduate Program in Computational Biology and BioinformaticsYale UniversityNew HavenConnecticutUSA
- Integrated Graduate Program in Physical and Engineering BiologyYale UniversityNew HavenConnecticutUSA
- Department of Mechanical Engineering and Materials ScienceYale UniversityNew HavenConnecticutUSA
- Department of PhysicsYale UniversityNew HavenConnecticutUSA
- Department of Applied PhysicsYale UniversityNew HavenConnecticutUSA
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10
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Levine ZA, Teranishi K, Okada AK, Langen R, Shea JE. The Mitochondrial Peptide Humanin Targets but Does Not Denature Amyloid Oligomers in Type II Diabetes. J Am Chem Soc 2019; 141:14168-14179. [DOI: 10.1021/jacs.9b04995] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Zachary A. Levine
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut 06520, United States
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, Connecticut 06520, United States
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11
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Levine ZA. Targeting Soluble Amyloid Oligomers in Alzheimer's Disease through Disordered Prion Peptides. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.2671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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12
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Oi C, Treado JD, Levine ZA, Lim CS, Knecht KM, Xiong Y, O'Hern CS, Regan L. A threonine zipper that mediates protein-protein interactions: Structure and prediction. Protein Sci 2018; 27:1969-1977. [PMID: 30198622 PMCID: PMC6201716 DOI: 10.1002/pro.3505] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Revised: 08/31/2018] [Accepted: 09/05/2018] [Indexed: 01/31/2023]
Abstract
We present the structure of an engineered protein-protein interface between two beta barrel proteins, which is mediated by interactions between threonine (Thr) residues. This Thr zipper structure suggests that the protein interface is stabilized by close-packing of the Thr residues, with only one intermonomer hydrogen bond (H-bond) between two of the Thr residues. This Thr-rich interface provides a unique opportunity to study the behavior of Thr in the context of many other Thr residues. In previous work, we have shown that the side chain (χ1 ) dihedral angles of interface and core Thr residues can be predicted with high accuracy using a hard sphere plus stereochemical constraint (HS) model. Here, we demonstrate that in the Thr-rich local environment of the Thr zipper structure, we are able to predict the χ1 dihedral angles of most of the Thr residues. Some, however, are not well predicted by the HS model. We therefore employed explicitly solvated molecular dynamics (MD) simulations to further investigate the side chain conformations of these residues. The MD simulations illustrate the role that transient H-bonding to water, in combination with steric constraints, plays in determining the behavior of these Thr side chains. Broader Audience Statement: Protein-protein interactions are critical to life and the search for ways to disrupt adverse protein-protein interactions involved in disease is an ongoing area of drug discovery. We must better understand protein-protein interfaces, both to be able to disrupt existing ones and to engineer new ones for a variety of biotechnological applications. We have discovered and characterized an artificial Thr-rich protein-protein interface. This novel interface demonstrates a heretofore unknown property of Thr-rich surfaces: mediating protein-protein interactions.
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Affiliation(s)
- Curran Oi
- Department of Molecular Biophysics and BiochemistryYale UniversityNew HavenConnecticut06520
- Integrated Graduate Program in Physical and Engineering BiologyYale UniversityNew HavenConnecticut06520
| | - John D. Treado
- Integrated Graduate Program in Physical and Engineering BiologyYale UniversityNew HavenConnecticut06520
- Department of Mechanical Engineering and Materials ScienceYale UniversityNew HavenConnecticut06520
| | - Zachary A. Levine
- Department of Molecular Biophysics and BiochemistryYale UniversityNew HavenConnecticut06520
- Department of PathologyYale School of MedicineNew HavenConnecticut06520
| | - Christopher S. Lim
- Department of Molecular Biophysics and BiochemistryYale UniversityNew HavenConnecticut06520
| | - Kirsten M. Knecht
- Department of Molecular Biophysics and BiochemistryYale UniversityNew HavenConnecticut06520
| | - Yong Xiong
- Department of Molecular Biophysics and BiochemistryYale UniversityNew HavenConnecticut06520
| | - Corey S. O'Hern
- Integrated Graduate Program in Physical and Engineering BiologyYale UniversityNew HavenConnecticut06520
- Department of Mechanical Engineering and Materials ScienceYale UniversityNew HavenConnecticut06520
- Department of PhysicsYale UniversityNew HavenConnecticut06520
- Department of Applied PhysicsYale UniversityNew HavenConnecticut06520
| | - Lynne Regan
- Department of Molecular Biophysics and BiochemistryYale UniversityNew HavenConnecticut06520
- Integrated Graduate Program in Physical and Engineering BiologyYale UniversityNew HavenConnecticut06520
- Department of ChemistryYale UniversityNew HavenConnecticut06520
- Institute of Quantitative BiologyBiochemistry and Biotechnology, Center for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh
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13
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Levine ZA. Membrane Permeabilizing Electric Fields Disrupt Water Channel Function and Selectivity. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.3332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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14
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Wójcik S, Birol M, Rhoades E, Miranker AD, Levine ZA. Targeting the Intrinsically Disordered Proteome Using Small-Molecule Ligands. Methods Enzymol 2018; 611:703-734. [DOI: 10.1016/bs.mie.2018.09.036] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Seo S, Lee DW, Ahn JS, Cunha K, Filippidi E, Ju SW, Shin E, Kim BS, Levine ZA, Lins RD, Israelachvili JN, Waite JH, Valentine MT, Shea JE, Ahn BK. Significant Performance Enhancement of Polymer Resins by Bioinspired Dynamic Bonding. Adv Mater 2017; 29:10.1002/adma.201703026. [PMID: 28833661 PMCID: PMC5640498 DOI: 10.1002/adma.201703026] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 06/22/2017] [Indexed: 05/09/2023]
Abstract
Marine mussels use catechol-rich interfacial mussel foot proteins (mfps) as primers that attach to mineral surfaces via hydrogen, metal coordination, electrostatic, ionic, or hydrophobic bonds, creating a secondary surface that promotes bonding to the bulk mfps. Inspired by this biological adhesive primer, it is shown that a ≈1 nm thick catecholic single-molecule priming layer increases the adhesion strength of crosslinked polymethacrylate resin on mineral surfaces by up to an order of magnitude when compared with conventional primers such as noncatecholic silane- and phosphate-based grafts. Molecular dynamics simulations confirm that catechol groups anchor to a variety of mineral surfaces and shed light on the binding mode of each molecule. Here, a ≈50% toughness enhancement is achieved in a stiff load-bearing polymer network, demonstrating the utility of mussel-inspired bonding for processing a wide range of polymeric interfaces, including structural, load-bearing materials.
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Affiliation(s)
- Sungbaek Seo
- Marine Science Institute, University of California, Santa Barbara, CA, 93106, USA
- Materials Research Laboratory, Materials Research Science and Engineering Center, University of California, Santa Barbara, CA, 93106, USA
- Biomaterials Science, Pusan National University, Miryang, 627-706, South Korea
| | - Dong Woog Lee
- Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan, 689-798, South Korea
- Chemical Engineering, University of California, Santa Barbara, CA, 93106, USA
| | - Jin Soo Ahn
- Marine Science Institute, University of California, Santa Barbara, CA, 93106, USA
- Dental Research Institute and Biomaterials Science, Dentistry, Seoul National University, Seoul, 110-749, South Korea
| | - Keila Cunha
- Marine Science Institute, University of California, Santa Barbara, CA, 93106, USA
- Fundamental Chemistry, Federal University of Pernambuco, Recife, PE, 50740-670, Brazil
- Chemistry and Biochemistry, University of California, Santa Barbara, CA, 93106, USA
| | - Emmanouela Filippidi
- Materials Research Laboratory, Materials Research Science and Engineering Center, University of California, Santa Barbara, CA, 93106, USA
- Mechanical Engineering, University of California, Santa Barbara, CA, 93106, USA
| | - Sung Won Ju
- Dental Research Institute and Biomaterials Science, Dentistry, Seoul National University, Seoul, 110-749, South Korea
| | - Eeseul Shin
- Chemistry, Ulsan National Institute of Science and Technology, Ulsan, 689-798, South Korea
| | - Byeong-Su Kim
- Chemistry, Ulsan National Institute of Science and Technology, Ulsan, 689-798, South Korea
| | - Zachary A Levine
- Chemistry and Biochemistry, University of California, Santa Barbara, CA, 93106, USA
| | - Roberto D Lins
- Fundamental Chemistry, Federal University of Pernambuco, Recife, PE, 50740-670, Brazil
- Aggeu Magalhaes Institute, Oswaldo Cruz Foundation, Recife, PE, 50670-465, Brazil
| | - Jacob N Israelachvili
- Materials Research Laboratory, Materials Research Science and Engineering Center, University of California, Santa Barbara, CA, 93106, USA
- Chemical Engineering, University of California, Santa Barbara, CA, 93106, USA
| | - J Herbert Waite
- Marine Science Institute, University of California, Santa Barbara, CA, 93106, USA
- Materials Research Laboratory, Materials Research Science and Engineering Center, University of California, Santa Barbara, CA, 93106, USA
| | - Megan T Valentine
- Materials Research Laboratory, Materials Research Science and Engineering Center, University of California, Santa Barbara, CA, 93106, USA
- Mechanical Engineering, University of California, Santa Barbara, CA, 93106, USA
| | - Joan Emma Shea
- Chemistry and Biochemistry, University of California, Santa Barbara, CA, 93106, USA
| | - B Kollbe Ahn
- Marine Science Institute, University of California, Santa Barbara, CA, 93106, USA
- Materials Research Laboratory, Materials Research Science and Engineering Center, University of California, Santa Barbara, CA, 93106, USA
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16
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Levine ZA, Shea JE. Simulations of disordered proteins and systems with conformational heterogeneity. Curr Opin Struct Biol 2016; 43:95-103. [PMID: 27988422 DOI: 10.1016/j.sbi.2016.11.006] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 11/07/2016] [Indexed: 12/29/2022]
Abstract
Intrinsically disordered proteins (IDPs) and protein regions can facilitate a wide variety of complex physiological processes such as binding, signaling, and formation of membraneless organelles. They can however also play pathological roles by aggregating into cytotoxic oligomers and fibrils. Characterizing the structure and function of disordered proteins is an onerous task, primarily because these proteins adopt transient structures, which are difficult to capture in experiments. Simulations have emerged as a powerful tool for interpreting and augmenting experimental measurements of IDPs. In this review we focus on computer simulations of disordered protein structures, functions, assemblies, and emerging questions that, taken together, give an overview of the field as it exists today.
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Affiliation(s)
- Zachary A Levine
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA 93106, USA; Department of Physics, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA 93106, USA; Department of Physics, University of California Santa Barbara, Santa Barbara, CA 93106, USA.
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17
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Das S, Lee BH, Linstadt RTH, Cunha K, Li Y, Kaufman Y, Levine ZA, Lipshutz BH, Lins RD, Shea JE, Heeger AJ, Ahn BK. Molecularly Smooth Self-Assembled Monolayer for High-Mobility Organic Field-Effect Transistors. Nano Lett 2016; 16:6709-6715. [PMID: 27673480 DOI: 10.1021/acs.nanolett.6b03860] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Despite the need for molecularly smooth self-assembled monolayers (SAMs) on silicon dioxide surfaces (the most common dielectric surface), current techniques are limited to nonideal silane grafting. Here, we show unique bioinspired zwitterionic molecules forming a molecularly smooth and uniformly thin SAM in "water" in <1 min on various dielectric surfaces, which enables a dip-coating process that is essential for organic electronics to become reality. This monomolecular layer leads to high mobility of organic field-effect transistors (OFETs) based on various organic semiconductors and source/drain electrodes. A combination of experimental and computational techniques confirms strong adsorption (Wad > 20 mJ m-2), uniform thickness (∼0.5 or ∼1 nm) and orientation (all catechol head groups facing the oxide surface) of the "monomolecular" layers. This robust (strong adsorption), rapid, and green SAM represents a promising advancement toward the next generation of nanofabrication compared to the current nonuniform and inconsistent polysiloxane-based SAM involving toxic chemicals, long processing time (>10 h), or heat (>80 °C).
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Affiliation(s)
| | | | | | - Keila Cunha
- Fundamental Chemistry, Federal University of Pernambuco , Recife, Pernambuco 50740-670, Brazil
| | | | - Yair Kaufman
- Zuckerberg Institute for Water Research, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev , Sede Boqer Campus, 84990 Midreshet Ben-Gurion, Israel
| | | | | | - Roberto D Lins
- Fundamental Chemistry, Federal University of Pernambuco , Recife, Pernambuco 50740-670, Brazil
- Aggeu Magalhães Research Center, Oswaldo Cruz Foundation, Recife, Pernambuco 50740-465, Brazil
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18
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Abstract
Using a combination of molecular dynamics simulations and experiments we examined the interactions of alkanes and phospholipids at charged interfaces in order to understand how interfacial charge densities affect the association of these two representative molecules with electrodes. Consistent with theory and experiment, these model systems reveal interfacial associations mediated through a combination of Coulombic and van der Waals forces. van der Waals forces, in particular, mediate rapid binding of decane to neutral electrodes. No decane binding was observed at high surface charge densities because of interfacial water polarization, which screens hydrophobic attractions. The positively charged choline moiety of the phospholipid palmitoyloleoylphosphatidylcholine (POPC) is primarily responsible for POPC attraction by a moderately negatively charged electrode. The hydrocarbon tails of POPC interact with the hydrophobic electrode interface similarly to decane. Previously reported electrochemical results confirm these findings by demonstrating bipolar displacement currents from PC vesicles adhering to moderately negatively charged interfaces, originating from the choline interactions observed in simulations. At more negatively charged interfaces, choline-to-surface binding was stronger. In both simulations and experiments the maximal interaction of anionic PS occurs with a positively charged interface, provided that the electrostatic forces outweigh local Lennard-Jones interactions. Direct comparisons between the binding affinities measured in experiments and those obtained in simulations reveal previously unobserved atomic interactions that facilitate lipid vesicle adhesion to charged interfaces. Moreover, the implementation of a charged interface in molecular dynamics simulations provides an alternative method for the generation of large electric fields across phospholipid bilayers, especially for systems with periodic boundary conditions, and may be useful for simulations of membrane electropermeabilization.
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Affiliation(s)
| | - Nadica Ivošević DeNardis
- Division for Marine and Environmental Research, Ruđer Bošković Institute , 10000 Zagreb, Croatia
| | - P Thomas Vernier
- Frank Reidy Research Center for Bioelectrics, Old Dominion University , Norfolk, Virginia 23508, United States
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19
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Levine ZA, Okada A, Teranishi K, Langen R, Shea JE. Reducing IAPP Aggregation with Mitochondrial Humanin Peptides; Results from Simulations and Experiments. Biophys J 2016. [DOI: 10.1016/j.bpj.2015.11.990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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20
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Abstract
The simulation of protein aggregation poses several computational challenges due to the disparate time and lengths scales that are involved. This chapter focuses on the use of atomistically detailed simulations to probe the initial steps of aggregation, with an emphasis on the Tau peptide as a model system, run under a replica exchange molecular dynamics protocol.
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Affiliation(s)
- Joan-Emma Shea
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA, 93106, USA.
- Department of Physics, University of California Santa Barbara, Santa Barbara, CA, 93106, USA.
| | - Zachary A Levine
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
- Department of Physics, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
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21
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Zerze GH, Mullen RG, Levine ZA, Shea JE, Mittal J. To What Extent Does Surface Hydrophobicity Dictate Peptide Folding and Stability near Surfaces? Langmuir 2015; 31:12223-12230. [PMID: 26484800 DOI: 10.1021/acs.langmuir.5b03814] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Protein-surface interactions are ubiquitous in both the cellular setting and in modern bioengineering devices, but how such interactions impact protein stability is not well understood. We investigate the folding of the GB1 hairpin peptide in the presence of self-assembled monolayers and graphite like surfaces using replica exchange molecular dynamics simulations. By varying surface hydrophobicity, and decoupling direct protein-surface interactions from water-mediated interactions, we show that surface wettability plays a surprisingly minor role in dictating protein stability. For both the β-hairpin GB1 and the helical miniprotein TrpCage, adsorption and stability is largely dictated by the nature of the direct chemical interactions between the protein and the surface. Independent of the surface hydrophobicity profile, strong protein-surface interactions destabilize the folded structure while weak interactions stabilize it.
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Affiliation(s)
- Gül H Zerze
- Department of Chemical and Biomolecular Engineering, Lehigh University , Bethlehem, Pennsylvania 18015, United States
| | - Ryan G Mullen
- Department of Chemical Engineering, University of California , Santa Barbara, California 93106, United States
| | - Zachary A Levine
- Department of Chemistry and Biochemistry, University of California , Santa Barbara, California 93106, United States
- Department of Physics, University of California , Santa Barbara, California 93106
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, University of California , Santa Barbara, California 93106, United States
- Department of Physics, University of California , Santa Barbara, California 93106
| | - Jeetain Mittal
- Department of Chemical and Biomolecular Engineering, Lehigh University , Bethlehem, Pennsylvania 18015, United States
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22
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Affiliation(s)
- Zachary A. Levine
- Department
of Physics, University of California Santa Barbara, Santa Barbara, California 93106, United States
- Department
of Chemistry and Biochemistry, University of California Santa Barbara, Santa
Barbara, California 93106, United States
| | - Sean A. Fischer
- Department
of Chemical Engineering, University of Washington, Seattle, Washington 98105, United States
| | - Joan-Emma Shea
- Department
of Physics, University of California Santa Barbara, Santa Barbara, California 93106, United States
- Department
of Chemistry and Biochemistry, University of California Santa Barbara, Santa
Barbara, California 93106, United States
| | - Jim Pfaendtner
- Department
of Chemical Engineering, University of Washington, Seattle, Washington 98105, United States
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23
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Vernier PT, Levine ZA, Ho MC, Xiao S, Semenov I, Pakhomov AG. Picosecond and Terahertz Perturbation of Interfacial Water and Electropermeabilization of Biological Membranes. J Membr Biol 2015; 248:837-47. [PMID: 25796485 DOI: 10.1007/s00232-015-9788-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 03/10/2015] [Indexed: 01/19/2023]
Abstract
Non-thermal probing and stimulation with subnanosecond electric pulses and terahertz electromagnetic radiation may lead to new, minimally invasive diagnostic and therapeutic procedures and to methods for remote monitoring and analysis of biological systems, including plants, animals, and humans. To effectively engineer these still-emerging tools, we need an understanding of the biophysical mechanisms underlying the responses that have been reported to these novel stimuli. We show here that subnanosecond (≤500 ps) electric pulses induce action potentials in neurons and cause calcium transients in neuroblastoma-glioma hybrid cells, and we report complementary molecular dynamics simulations of phospholipid bilayers in electric fields in which membrane permeabilization occurs in less than 1 ns. Water dipoles in the interior of these model membranes respond in less than 1 ps to permeabilizing electric potentials by aligning in the direction of the field, and they re-orient at terahertz frequencies to field reversals. The mechanism for subnanosecond lipid electropore formation is similar to that observed on longer time scales-energy-minimizing intrusions of interfacial water into the membrane interior and subsequent reorganization of the bilayer into hydrophilic, conductive structures.
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Affiliation(s)
- P Thomas Vernier
- Frank Reidy Research Center for Bioelectrics, Old Dominion University, 4211 Monarch Way, Norfolk, VA, 23508, USA,
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24
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Ho MC, Casciola M, Levine ZA, Vernier PT. Molecular dynamics simulations of ion conductance in field-stabilized nanoscale lipid electropores. J Phys Chem B 2013; 117:11633-40. [PMID: 24001115 DOI: 10.1021/jp401722g] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular dynamics (MD) simulations of electrophoretic transport of monovalent ions through field-stabilized electropores in POPC lipid bilayers permit systematic characterization of the conductive properties of lipid nanopores. The radius of the electropore can be controlled by the magnitude of the applied sustaining external electric field, which also drives the transport of ions through the pore. We examined pore conductances for two monovalent salts, NaCl and KCl, at physiological concentrations. Na(+) conductance is significantly less than K(+) and Cl(-) conductance and is a nonlinear function of pore radius over the range of pore radii investigated. The single pore electrical conductance of KCl obtained from MD simulation is comparable to experimental values measured by chronopotentiometry.
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Affiliation(s)
- Ming-Chak Ho
- Department of Physics and Astronomy, Dornsife College of Letters, Arts, and Sciences, University of Southern California , Los Angeles, California, United States
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25
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Romeo S, Wu YH, Levine ZA, Gundersen MA, Vernier PT. Water influx and cell swelling after nanosecond electropermeabilization. Biochimica et Biophysica Acta (BBA) - Biomembranes 2013; 1828:1715-22. [DOI: 10.1016/j.bbamem.2013.03.007] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Revised: 02/20/2013] [Accepted: 03/01/2013] [Indexed: 10/27/2022]
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26
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Tokman M, Lee JH, Levine ZA, Ho MC, Colvin ME, Vernier PT. Electric field-driven water dipoles: nanoscale architecture of electroporation. PLoS One 2013; 8:e61111. [PMID: 23593404 PMCID: PMC3623848 DOI: 10.1371/journal.pone.0061111] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Accepted: 03/05/2013] [Indexed: 12/02/2022] Open
Abstract
Electroporation is the formation of permeabilizing structures in the cell membrane under the influence of an externally imposed electric field. The resulting increased permeability of the membrane enables a wide range of biological applications, including the delivery of normally excluded substances into cells. While electroporation is used extensively in biology, biotechnology, and medicine, its molecular mechanism is not well understood. This lack of knowledge limits the ability to control and fine-tune the process. In this article we propose a novel molecular mechanism for the electroporation of a lipid bilayer based on energetics analysis. Using molecular dynamics simulations we demonstrate that pore formation is driven by the reorganization of the interfacial water molecules. Our energetics analysis and comparisons of simulations with and without the lipid bilayer show that the process of poration is driven by field-induced reorganization of water dipoles at the water-lipid or water-vacuum interfaces into more energetically favorable configurations, with their molecular dipoles oriented in the external field. Although the contributing role of water in electroporation has been noted previously, here we propose that interfacial water molecules are the main players in the process, its initiators and drivers. The role of the lipid layer, to a first-order approximation, is then reduced to a relatively passive barrier. This new view of electroporation simplifies the study of the problem, and opens up new opportunities in both theoretical modeling of the process and experimental research to better control or to use it in new, innovative ways.
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Affiliation(s)
- Mayya Tokman
- School of Natural Sciences, University of California Merced, Merced, California, USA.
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27
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Levine ZA, Ivošević DeNardis N, Vernier PT. Molecular Dynamics Interactions between Silicon Electrodes and Phospholipids. Biophys J 2013. [DOI: 10.1016/j.bpj.2012.11.1860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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28
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Levine ZA, Vernier PT. Electropore Dynamics in Time-Dependent Electric Fields. Biophys J 2012. [DOI: 10.1016/j.bpj.2011.11.2190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
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29
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Ho MC, Levine ZA, Vernier PT. Molecular Dynamics Comparison of Electroporation in Water-Vacuum-Water and Lipid Bilayer System. Biophys J 2012. [DOI: 10.1016/j.bpj.2011.11.2178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
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30
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Levine ZA, Vernier PT. Temperature Modulation of the Life Cycles of Phospholipid Bilayer Electropores. Biophys J 2011. [DOI: 10.1016/j.bpj.2010.12.1032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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31
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Knecht V, Levine ZA, Vernier PT. Electrophoresis of neutral oil in water. J Colloid Interface Sci 2010; 352:223-31. [DOI: 10.1016/j.jcis.2010.07.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2010] [Revised: 06/25/2010] [Accepted: 07/01/2010] [Indexed: 11/30/2022]
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32
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Lee JH, Levine ZA, Vernier PT, Tokman M, Colvin ME. Electric Field Effects on Water and Water-Vacuum Interfaces in Molecular Dynamics Simulations. Biophys J 2010. [DOI: 10.1016/j.bpj.2009.12.2081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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33
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Levine ZA, Ziegler MJ, Vernier PT. Life Cycle of an Electropore: A Molecular Dynamics Investigation of the Electroporation of Heterogeneous Lipid Bilayers (PC:PS) In the Presence of Calcium Ions. Biophys J 2010. [DOI: 10.1016/j.bpj.2009.12.2084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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34
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Vernier PT, Levine ZA, Wu YH, Joubert V, Ziegler MJ, Mir LM, Tieleman DP. Electroporating fields target oxidatively damaged areas in the cell membrane. PLoS One 2009; 4:e7966. [PMID: 19956595 PMCID: PMC2779261 DOI: 10.1371/journal.pone.0007966] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2009] [Accepted: 10/23/2009] [Indexed: 11/18/2022] Open
Abstract
Reversible electropermeabilization (electroporation) is widely used to facilitate the introduction of genetic material and pharmaceutical agents into living cells. Although considerable knowledge has been gained from the study of real and simulated model membranes in electric fields, efforts to optimize electroporation protocols are limited by a lack of detailed understanding of the molecular basis for the electropermeabilization of the complex biomolecular assembly that forms the plasma membrane. We show here, with results from both molecular dynamics simulations and experiments with living cells, that the oxidation of membrane components enhances the susceptibility of the membrane to electropermeabilization. Manipulation of the level of oxidative stress in cell suspensions and in tissues may lead to more efficient permeabilization procedures in the laboratory and in clinical applications such as electrochemotherapy and electrotransfection-mediated gene therapy.
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Affiliation(s)
- P Thomas Vernier
- Ming Hsieh Department of Electrical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, California, United States of America.
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35
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36
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Fabrizio PA, Schmidt JA, Clemente FR, Lankiewicz LA, Levine ZA. Acute effects of therapeutic ultrasound delivered at varying parameters on the blood flow velocity in a muscular distribution artery. J Orthop Sports Phys Ther 1996; 24:294-302. [PMID: 8902681 DOI: 10.2519/jospt.1996.24.5.294] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Therapeutic modalities that alter hemodynamic parameters may have a dramatic impact on the viability of living tissues. The purpose of the current study was to investigate the response of blood flow velocity to various treatment parameters of therapeutic ultrasound. Twenty healthy volunteers attended six randomly selected, 15-minute treatment sessions of the following parameters: Tx-1 = 1.0 MHz at 1.5 W/cm2, Tx-2 = 1.0 MHz at 1.0 W/cm2; Tx-3 = 3.0 MHz at 1.2 W/cm2; Tx-4 = 3.0 MHz at 1.0 W/cm2, Tx-5 = sham; and Tx-6 = control. Ultrasound was applied to a circular area over the triceps surae muscle mass. Blood flow velocity in the popliteal artery was assessed after 5, 10, and 15 minutes of ultrasound and at two posttreatment intervals via a dual frequency, bidirectional ultrasound Doppler. A two-factor analysis of variance (p < or = 0.05) with repeated measures for treatment and time was performed on the data. Groups Tx-1 and Tx-2 showed significant increases in blood flow velocity when compared with the control and all other groups. The sham group showed significant increases in blood flow velocity when compared with the control group. Group Tx-3 and Tx-4 showed no significant change when compared with the sham condition. The results of the current study indicate that 1.0 MHz ultrasound delivered at 1.0 and 1.5 W/cm2 to the triceps surae musculature as described in the present study can increase the blood flow velocity in the popliteal artery.
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Affiliation(s)
- P A Fabrizio
- Duquesne University, Rangos School of Health Sciences, Department of Physical Therapy, Pittsburgh, PA 15282, USA
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