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 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.

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.

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.

De novo design, synthesis and study of albebetin, a polypeptide with a predetermined three-dimensional structure

1992 ◽  
Vol 225 (4) ◽  
pp. 927-931 ◽  
Author(s):  
A.N. Fedorov ◽  
D.A. Dolgikh ◽  
V.V. Chemeris ◽  
B.K. Chernov ◽  
A.V. Finkelstein ◽  
...  
Keyword(s):  
De Novo ◽  
Three Dimensional ◽  
De Novo Design ◽  
Dimensional Structure ◽  
Design Synthesis ◽  
Three Dimensional Structure

scholarly journals Robust de novo design of protein binding proteins from target structural information alone

2021 ◽  
Author(s):  
Longxing Cao ◽  
Brian Coventry ◽  
Inna Goreshnik ◽  
Buwei Huang ◽  
Joon Sung Park ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Binding Proteins ◽  
De Novo ◽  
Structural Information ◽  
Three Dimensional ◽  
Computational Design ◽  
De Novo Design ◽  
Dimensional Structure ◽  
Binding Modes ◽  
Large Space

The design of proteins that bind to a specific site on the surface of a target protein using no information other than the three-dimensional structure of the target remains an outstanding challenge. We describe a general solution to this problem which starts with a broad exploration of the very large space of possible binding modes and interactions, and then intensifies the search in the most promising regions. We demonstrate its very broad applicability by de novo design of binding proteins to 12 diverse protein targets with very different shapes and surface properties. Biophysical characterization shows that the binders, which are all smaller than 65 amino acids, are hyperstable and bind their targets with nanomolar to picomolar affinities. We succeeded in solving crystal structures of four of the binder-target complexes, and all four are very close to the corresponding computational design models. Experimental data on nearly half a million computational designs and hundreds of thousands of point mutants provide detailed feedback on the strengths and limitations of the method and of our current understanding of protein-protein interactions, and should guide improvement of both. Our approach now enables targeted design of binders to sites of interest on a wide variety of proteins for therapeutic and diagnostic applications.

The three-dimensional structure of crystalline porcine pancreatic elastase

1970 ◽  
Vol 257 (813) ◽  
pp. 111-118 ◽  
Keyword(s):  
Amino Acid ◽  
Catalytic Mechanism ◽  
Polypeptide Chain ◽  
Molecular Model ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Side Chains ◽  
Peptide Bonds ◽  
Single Polypeptide Chain ◽  
Single Polypeptide

Elastase is a proteolytic enzyme obtained from pig pancreas, which shows a high degree of amino acid sequence homology with other serine proteinases, including bovine trypsin and chymotrypsin (Hartley, this volume, p. 77). It consists of a single polypeptide chain of 240 residues, which corresponds to the single polypeptide chain of trypsin, and the B and C chains of chymotrypsin. Elastase possesses a common catalytic mechanism with these enzymes but differs from them in its substrate specificity, cleaving peptide bonds on the carboxyl terminal side of amino acid residues lacking charged or aromatic side chains (Naughton & Sanger 1961). Several workers have suggested that homologous enzymes with common catalytic mechanisms have very similar tertiary structures. This prediction was supported by Blow and his co-workers, who found that the two disulphide bridges present in trypsin, but absent in chymotrypsin, could be built into the molecular model of a-chymotrypsin with little or no distortion of the polypeptide chain (Sigler, Blow, Matthews & Henderson 1968), and by Hartley (this volume, p. 77) who has shown that the trypsin and elastase side chains can be substituted for those present in a skeletal molecular model of a-chymotrypsin with no gross distortions of the polypeptide chain.

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 A Novel Missense Variant in the Gene PPP2R5D Causes a Rare Neurodevelopmental Disorder with Increased Phenotype

2021 ◽  
Vol 2021 ◽  
pp. 1-7
Author(s):  
Lulu Yan ◽  
Ru Shen ◽  
Zongfu Cao ◽  
Chunxiao Han ◽  
Yuxin Zhang ◽  
...  
Keyword(s):  
De Novo ◽  
Genetic Disorder ◽  
Neurodevelopmental Disorder ◽  
Three Dimensional ◽  
Missense Variant ◽  
Pathogenic Variant ◽  
Dimensional Structure ◽  
Chinese Family ◽  
Speech Impairment ◽  
Pathogenic Variants

PPP2R5D-related neurodevelopmental disorder, which is mainly caused by de novo missense variants in the PPP2R5D gene, is a rare autosomal dominant genetic disorder with about 100 patients and a total of thirteen pathogenic variants known to exist globally so far. Here, we present a 24-month-old Chinese boy with developmental delay and other common clinical characteristics of PPP2R5D-related neurodevelopmental disorder including hypotonia, macrocephaly, intellectual disability, speech impairment, and behavioral abnormality. Trio-whole exome sequencing (WES) and Sanger sequencing were performed to identify the causal gene variant. The pathogenicity of the variant was evaluated using bioinformatics tools. We identified a novel pathogenic variant in the PPP2R5D gene (c.620G>T, p.Trp207Leu). The variant is located in the variant hotspot region of this gene and is predicted to cause PPP2R5D protein dysfunction due to an increase in local hydrophobicity and unstable three-dimensional structure. We report a novel pathogenic variant of PPP2R5D associated with PPP2R5D-related neurodevelopmental disorder from a Chinese family. Our findings expanded the phenotypic and mutational spectrum of PPP2R5D-related neurodevelopmental disorder.

Enhancement of oligomeric stability by covalent linkage and its application to the human p53tet domain: thermodynamics and biological implications

2007 ◽  
Vol 35 (6) ◽  
pp. 1574-1578 ◽  
Author(s):  
G.M.K. Poon
Keyword(s):  
De Novo ◽  
Universal Method ◽  
Oligomeric State ◽  
Covalent Linkage ◽  
Oligomeric Proteins ◽  
Single Polypeptide Chain ◽  
Tumour Suppressor Protein ◽  
Cross Links ◽  
Irreversible Aggregation ◽  
Single Polypeptide

The formation of oligomeric proteins proceeds at a major cost of reducing the translational and rotational entropy for their subunits in order to form the stabilizing interactions found in the oligomeric state. Unlike site-directed mutations, covalent linkage of subunits represents a generically applicable strategy for enhancing oligomeric stability by reducing the entropic driving force for dissociation. Although this can be realized by introducing de novo disulfide cross-links between subunits, issues with irreversible aggregation limit the utility of this approach. In contrast, tandem linkage of subunits in a single polypeptide chain offers a universal method of pre-paying the entropic cost of oligomer formation. In the present paper, thermodynamic, structural and experimental aspects of designing and characterizing tandem-linked oligomers are discussed with reference to engineering a stabilized tetramer of the oligomerization domain of the human p53 tumour-suppressor protein by tandem dimerization.

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