Three-Dimensional Packing Defects in Lipid Membrane as a Function of Membrane Order

2020 ◽  
Vol 16 (12) ◽  
pp. 7800-7816
Author(s):  
Madhusmita Tripathy ◽  
Subasini Thangamani ◽  
Anand Srivastava
Keyword(s):  
Lipid Membrane ◽  
Three Dimensional ◽  
Membrane Order ◽  
Packing Defects

scholarly journals Three-dimensional structure of neuropeptide Y pre-pro-peptide to reveal its interaction with lipid membrane

2016 ◽  
Vol 22 (S3) ◽  
pp. 1128-1129
Author(s):  
Li Xing ◽  
Ming-Siao Hsiao ◽  
Zhi-Feng Kuang ◽  
Yen Ngo ◽  
Steve Kim ◽  
...  
Keyword(s):  
Neuropeptide Y ◽  
Lipid Membrane ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Three Dimensional Structure

scholarly journals 3D Packing Defects in Lipid Membrane as a Function of Membrane Order

2019 ◽  
Author(s):  
Madhusmita Tripathy ◽  
Anand Srivastava
Keyword(s):  
Lipid Membrane ◽  
Membrane Binding ◽  
Computationally Efficient ◽  
Protein Motifs ◽  
Liquid Phases ◽  
Preferential Localization ◽  
Peripheral Proteins ◽  
Packing Defects ◽  
3D Packing ◽  
Key Steps

AbstractLipid membrane packing defects are considered as essential parameter that regulates specific membrane binding of several peripheral proteins. In absence of direct experimental characterization, lipid packing defects and their role in the binding of peripheral proteins are generally investigated through computational studies, which have been immensely successful in unraveling the key steps of the membrane-binding process. However, packing defects are calculated using 2-dimensional projections and the crucial information on their depths is generally overlooked. Here we present a simple yet computationally efficient algorithm, which identifies these defects in 3-dimensions. We employ the algorithm to understand the nature of packing defects in flat bilayer membranes exhibiting liquid-ordered (Lo), liquid-disordered (Ld) and co-existing Lo/Ld phases. Our results indicate the presence of shallower and smaller defects in the Lo phase membranes as compared to the defects in Ld and mixed Lo/Ld phase membranes. Such analyses can elucidate the molecular scale mechanisms that drive the preferential localization of certain proteins to either of the liquid phases or their interface. Moreover, on the methodology front, our analyses suggest that the projection based 2-dimensional calculation of packing defects might result in inaccurate quantification of their sizes - a very important feature for membrane association of protein motifs, thus advocating the importance of the 3-dimensional calculations.

scholarly journals Membrane-Binding Peptides for Extracellular Vesicles On-Chip Analysis

2020 ◽  
Author(s):  
Alessandro Gori ◽  
Alessandro Romanato ◽  
Greta Bergamaschi ◽  
Alessandro Strada ◽  
Paola Gagni ◽  
...  
Keyword(s):  
Extracellular Vesicles ◽  
Lipid Membrane ◽  
Binding Capacity ◽  
Microarray Platform ◽  
Label Free ◽  
New Class ◽  
Associated Proteins ◽  
Packing Defects ◽  
Binding Peptides ◽  
On Chip

Small extracellular vesicles (EVs) present fairly distinctive lipid membrane features in the extracellular environment. These include high curvature, lipid packing defects and a relative abundance in lipids such as phosphatidylserine and ceramide. EVs membrane could be then considered as a "universal" marker, alternative or complementary to traditional characteristic surface-associated proteins. Here we introduce the use of membrane sensing peptides as new, highly efficient ligands for EVs capturing onto bioanalytical chips to directly integrate EVs capturing and analysis on a microarray platform, even using serum without pre-isolation steps. EVs were analyzed by label-free, single particle counting and by fluorescence co-localization immune-staining with labelled anti-CD9/anti-CD63/anti-CD81 antibodies. Peptides performed as selective yet general EVs baits and showed a binding capacity higher than anti-tetraspanins antibodies. Insights into surface chemistry for optimal peptide performance are also discussed, as capturing efficiency is strictly bound to probes surface orientation and multivalency effects. We anticipate that this new class of ligands, also due to the versatility and limited costs of synthetic peptides, may greatly enrich the molecular toolbox for EVs analysis.

scholarly journals De Novo Design of a Nanopore for DNA Detection that Incorporates a β-Hairpin Peptide

2021 ◽  
Author(s):  
Keisuke Shimizu ◽  
Batsaikhan Mijiddorj ◽  
Masataka Usami ◽  
Shuhei Yoshida ◽  
Shiori Akayama ◽  
...  
Keyword(s):  
Single Molecule ◽  
Protein Design ◽  
Lipid Membrane ◽  
De Novo ◽  
Three Dimensional ◽  
Bilayer Lipid Membrane ◽  
De Novo Design ◽  
Dimensional Structure ◽  
Practical Applications ◽  
Single Molecule Level

Abstract The amino acid sequence of a protein encodes information on its three-dimensional structure and specific functionality. De novo protein design has emerged as a method to manipulate the primary structure for the development of artificial proteins and peptides with desired functionality. This paper describes the de novo design of a pore-forming peptide that has a β-hairpin structure and assembles to form a stable nanopore in a bilayer lipid membrane. This large synthetic nanopore is an entirely artificial device with practical applications. This peptide, named SV28, forms nanopore structures ranging from 1.6 to 6.2 nm in diameter assembled from 7 to 18 monomers. The nanopore formed with a diameter of 5 nm is able to detect long double-stranded DNA (dsDNA) with 1 kbp length. Moreover, the larger sized nanopore can discriminate and human telomeric DNA (G-quadruplex, G4). The blocking current signals allowed us to investigate the translocation behavior of dsDNA or G4 structure at the single molecule level. Such de novo design of peptide sequences has the potential to create novel nanopores, which would be applicable in molecular transporter between across lipid membrane.

De Novo Design of a Nanopore for DNA Detection Incorporating a β-hairpin Peptide

2020 ◽  
Author(s):  
Keisuke Shimizu ◽  
Batsaikhan Mijiddorj ◽  
Shuhei Yoshida ◽  
Shiori Akayama ◽  
Yoshio Hamada ◽  
...  
Keyword(s):  
Single Molecule ◽  
Protein Design ◽  
Lipid Membrane ◽  
De Novo ◽  
Three Dimensional ◽  
Bilayer Lipid Membrane ◽  
De Novo Design ◽  
Dimensional Structure ◽  
Practical Applications ◽  
Single Molecule Level

The amino acid sequence of a protein encodes information on its three-dimensional structure and specific functionality. De novo protein design has emerged as a method to manipulate the primary structure for the development of artificial proteins and peptides with desired functionality. This paper describes the de novo design of a pore-forming peptide that has a β-hairpin structure and assembles to form a stable nanopore in a bilayer lipid membrane. This large synthetic nanopore is an entirely artificial device with practical applications. This peptide, named SV28, forms nanopore structures ranging from 1.6 to 6.2 nm in diameter assembled from 7 to 18 monomers. The nanopore formed with a diameter of 5 nm is able to detect long double-stranded DNA (dsDNA) with 1 kbp length, and measurement of current signals allowed us to investigate the translocation behavior of dsDNA at the single molecule level. Such de novo design of peptide sequences has the potential to create assembled structure in lipid membrane such as novel nanopores, which would also be applicable in molecular transporter between inside and outside of lipid membrane.

Membrane-Binding Peptides for Extracellular Vesicles On-Chip Analysis

2019 ◽  
Author(s):  
Alessandro Gori ◽  
Alessandro Romanato ◽  
Greta Bergamaschi ◽  
Alessandro Strada ◽  
Paola Gagni ◽  
...  
Keyword(s):  
Extracellular Vesicles ◽  
Lipid Membrane ◽  
Binding Capacity ◽  
Microarray Platform ◽  
Label Free ◽  
New Class ◽  
Associated Proteins ◽  
Packing Defects ◽  
Binding Peptides ◽  
On Chip

Small extracellular vesicles (EVs) present fairly distinctive lipid membrane features in the extracellular environment. These include high curvature, lipid packing defects and a relative abundance in lipids such as phosphatidylserine and ceramide. EVs membrane could be then considered as a "universal" marker, alternative or complementary to traditional characteristic surface-associated proteins. Here we introduce the use of membrane sensing peptides as new, highly efficient ligands for EVs capturing onto bioanalytical chips to directly integrate EVs capturing and analysis on a microarray platform, even using serum without pre-isolation steps. EVs were analyzed by label-free, single particle counting and by fluorescence co-localization immune-staining with labelled anti-CD9/anti-CD63/anti-CD81 antibodies. Peptides performed as selective yet general EVs baits and showed a binding capacity higher than anti-tetraspanins antibodies. Insights into surface chemistry for optimal peptide performance are also discussed, as capturing efficiency is strictly bound to probes surface orientation and multivalency effects. We anticipate that this new class of ligands, also due to the versatility and limited costs of synthetic peptides, may greatly enrich the molecular toolbox for EVs analysis.

scholarly journals Photolithographic Fabrication of Microapertures with Well-Defined, Three-Dimensional Geometries for Suspended Lipid Membrane Studies

2013 ◽  
Vol 85 (19) ◽  
pp. 9078-9086 ◽  
Author(s):  
Christopher A. Baker ◽  
Leonard K. Bright ◽  
Craig A. Aspinwall
Keyword(s):  
Lipid Membrane ◽  
Three Dimensional

scholarly journals The insertion of human apolipoprotein H into phospholipid membranes: a monolayer study

1998 ◽  
Vol 335 (2) ◽  
pp. 225-232 ◽  
Author(s):  
Shao-Xiong WANG ◽  
Guo-ping CAI ◽  
Sen-fang SUI
Keyword(s):  
Lipid Membrane ◽  
Hydrophobic Interactions ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Heat Inactivation ◽  
Sequence Motif ◽  
Phospholipid Membranes ◽  
Human Apolipoprotein ◽  
Stable Domain ◽  
Apolipoprotein H

Apolipoprotein H (ApoH) is a plasma glycoprotein isolated from human serum. The interactions of ApoH with lipid membrane were reported to be essential for its physiological and pathogenic roles. In this paper we studied the ability of ApoH to insert into phospholipid membranes using the monolayer approach. The results show that ApoH is surface active and can insert into the lipid monolayers. The insertion ability of ApoH is stronger when a higher content of negatively charged lipids is present in the membrane. The acidic-pH and low-ionic-strength conditions will also enhance ApoH insertion, but these factors may not have much influence on the final insertion ability of ApoH, suggesting that, in the mechanism of ApoH insertion, not only electrostatic forces, but also hydrophobic interactions, are evidently involved. Modification by heat inactivation and reduction/alkylation does not change the critical insertion pressure (πc) of ApoH, suggesting a stable domain, maybe a linear sequence motif, but not the native three-dimensional structure of ApoH, is responsible for its insertion. The extent to which insertion of ApoH into phospholipid membranes may facilitate the ‘immune cleaning ’ of plasma liposomes is discussed.

scholarly journals De novo design of a nanopore for single-molecule detection that incorporates a β-hairpin peptide

2021 ◽  
Author(s):  
Keisuke Shimizu ◽  
Batsaikhan Mijiddorj ◽  
Masataka Usami ◽  
Ikuro Mizoguchi ◽  
Shuhei Yoshida ◽  
...  
Keyword(s):  
Single Molecule ◽  
Lipid Membrane ◽  
De Novo ◽  
Three Dimensional ◽  
Bilayer Lipid Membrane ◽  
De Novo Design ◽  
Dimensional Structure ◽  
Practical Applications ◽  
Single Polypeptide Chain ◽  
Single Polypeptide

AbstractThe amino-acid sequence of a protein encodes information on its three-dimensional structure and specific functionality. De novo design has emerged as a method to manipulate the primary structure for the development of artificial proteins and peptides with desired functionality. This paper describes the de novo design of a pore-forming peptide, named SV28, that has a β-hairpin structure and assembles to form a stable nanopore in a bilayer lipid membrane. This large synthetic nanopore is an entirely artificial device for practical applications. The peptide forms multidispersely sized nanopore structures ranging from 1.7 to 6.3 nm in diameter and can detect DNAs. To form a monodispersely sized nanopore, we redesigned the SV28 by introducing a glycine-kink mutation. The resulting redesigned peptide forms a monodisperse pore with a diameter of 1.7 nm leading to detection of a single polypeptide chain. Such de novo design of a β-hairpin peptide has the potential to create artificial nanopores, which can be size adjusted to a target molecule.

scholarly journals De Novo Design of a Nanopore for DNA Detection Incorporating a β-hairpin Peptide

2020 ◽  
Author(s):  
Keisuke Shimizu ◽  
Batsaikhan Mijiddorj ◽  
Shuhei Yoshida ◽  
Shiori Akayama ◽  
Yoshio Hamada ◽  
...  
Keyword(s):  
Single Molecule ◽  
Protein Design ◽  
Lipid Membrane ◽  
De Novo ◽  
Three Dimensional ◽  
Bilayer Lipid Membrane ◽  
De Novo Design ◽  
Dimensional Structure ◽  
Practical Applications ◽  
Single Molecule Level

The amino acid sequence of a protein encodes information on its three-dimensional structure and specific functionality. De novo protein design has emerged as a method to manipulate the primary structure for the development of artificial proteins and peptides with desired functionality. This paper describes the de novo design of a pore-forming peptide that has a β-hairpin structure and assembles to form a stable nanopore in a bilayer lipid membrane. This large synthetic nanopore is an entirely artificial device with practical applications. This peptide, named SV28, forms nanopore structures ranging from 1.6 to 6.2 nm in diameter assembled from 7 to 18 monomers. The nanopore formed with a diameter of 5 nm is able to detect long double-stranded DNA (dsDNA) with 1 kbp length, and measurement of current signals allowed us to investigate the translocation behavior of dsDNA at the single molecule level. Such de novo design of peptide sequences has the potential to create assembled structure in lipid membrane such as novel nanopores, which would also be applicable in molecular transporter between inside and outside of lipid membrane.

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