LIVIVO - Search results -

Search results

Result 1 - 10 of total 232

Search options

Article ; Online: Use of Phage Display and Other Molecular Display Methods for the Development of Monobodies.

Koide, Akiko / Koide, Shohei

Cold Spring Harbor protocols

2023

Abstract: Synthetic binding proteins are human-made binding proteins that use non-antibody proteins as the starting scaffold. Molecular display technologies, such as phage display, enable the construction of large combinatorial libraries and their efficient ... ...

Abstract	Synthetic binding proteins are human-made binding proteins that use non-antibody proteins as the starting scaffold. Molecular display technologies, such as phage display, enable the construction of large combinatorial libraries and their efficient sorting and, thus, are crucial for the development of synthetic binding proteins. Monobodies are the founding system of a set of synthetic binding proteins based on the fibronectin type III (FN3) domain. Since the original report in 1998, the monobody and related FN3-based systems have steadily been refined, and current methods are capable of rapidly generating potent and selective binding molecules to even challenging targets. The FN3 domain is small (∼90 amino acids) and autonomous and is structurally similar to the conventional immunoglobulin (Ig) domain. Unlike the Ig domain, however, the FN3 lacks a disulfide bond but is highly stable. These attributes of FN3 present unique opportunities and challenges in the design of phage and other display systems, combinatorial libraries, and library sorting strategies. This article reviews key technological innovations in the establishment of our monobody development pipeline, with an emphasis on phage display methodology. These give insights into the molecular mechanisms underlying molecular display technologies and protein-protein interactions, which should be broadly applicable to diverse systems intended for generating high-performance binding proteins.
Language	English
Publishing date	2023-05-03
Publishing country	United States
Document type	Journal Article
ISSN	1559-6095
ISSN (online)	1559-6095
DOI	10.1101/pdb.over107982
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: Repurposing off-the-shelf antihelix antibodies for enabling structural biology.

Koide, Shohei

Proceedings of the National Academy of Sciences of the United States of America

2019 Volume 116, Issue 36, Page(s) 17611–17613

MeSH term(s)	Antibodies ; Ear Auricle ; Ear, External ; Proteins
Chemical Substances	Antibodies ; Proteins
Language	English
Publishing date	2019-08-19
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Comment
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.1912643116
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 1148: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (1.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: Engineering Binders with Exceptional Selectivity.

Teng, Kai Wen / Koide, Akiko / Koide, Shohei

Methods in molecular biology (Clifton, N.J.)

2022 Volume 2491, Page(s) 143–154

Abstract: Molecular display technologies have enabled the generation of synthetic binders with high affinities against a variety of antigens. However, engineering binders with high selectivity is still a challenging task. Here, we illustrate points to consider in ... ...

Abstract	Molecular display technologies have enabled the generation of synthetic binders with high affinities against a variety of antigens. However, engineering binders with high selectivity is still a challenging task. Here, we illustrate points to consider in developing highly selective binders against antigens of interest. We describe a systematic strategy for sorting selective binders using the yeast display technology. Using the approach described, our group has overcome molecular recognition challenges and developed a series of synthetic binders with exceptional selectivity against diverse antigens.
MeSH term(s)	Antigens ; Peptide Library ; Protein Engineering ; Saccharomyces cerevisiae/genetics
Chemical Substances	Antigens ; Peptide Library
Language	English
Publishing date	2022-04-28
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-2285-8_8
Database	MEDical Literature Analysis and Retrieval System OnLINE

Full text online

Accessible to users with ZB MED library card

Order via subito

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Details ▾
- Full text online
- Order with fees

Article ; Online: β-Strand-mediated Domain-swapping in the Absence of Hydrophobic Core Repacking.

Kiya, Mikoto / Shiga, Shota / Ding, Peiwei / Koide, Shohei / Makabe, Koki

Journal of molecular biology

2023 Volume 436, Issue 2, Page(s) 168405

Abstract: Domain swapping is a process wherein a portion of a protein is exchanged with its counterpart in another copy of the molecule, resulting in the formation of homo-oligomers with concomitant repacking of a hydrophobic core. Here, we report domain swapping ... ...

Abstract	Domain swapping is a process wherein a portion of a protein is exchanged with its counterpart in another copy of the molecule, resulting in the formation of homo-oligomers with concomitant repacking of a hydrophobic core. Here, we report domain swapping triggered upon modifying a β-hairpin sequence within a single-layer β-sheet (SLB) of a model protein, OspA that did not involve the formation of a reorganized hydrophobic core. The replacement of two β-hairpin sequences with a Gly-Gly and shorteing of a β-hairpin resulted in a protein that formed two distinct crystal structures under similar conditions: one was monomeric, similar to the parental molecule, whereas the other was a domain-swapped dimer, mediated by an intermolecular β-sheet in the SLB portion. Based on the dimer interface structure, we replaced the Gly-Gly sequence with three-residue sequences that enable the formation of a consecutive intermolecular β-sheet, including the Cys-Thr-Cys sequence that formed a stable disulfide-linked dimer. These results provide new insights into protein folding, evolution, and the designability of protein structure.
MeSH term(s)	Protein Conformation, beta-Strand ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Hydrophobic and Hydrophilic Interactions ; Protein Domains
Language	English
Publishing date	2023-12-15
Publishing country	Netherlands
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, Non-U.S. Gov't
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2023.168405
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 867: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (1.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: Monobody Inhibitor Selective to the Phosphatase Domain of SHP2 and its Use as a Probe for Quantifying SHP2 Allosteric Regulation.

Sha, Fern / Kurosawa, Kohei / Glasser, Eliezra / Ketavarapu, Gayatri / Albazzaz, Samara / Koide, Akiko / Koide, Shohei

Journal of molecular biology

2023 Volume 435, Issue 8, Page(s) 168010

Abstract: SHP2 is a phosphatase/adaptor protein that plays an important role in various signaling pathways. Its mutations are associated with cancers and developmental diseases. SHP2 contains a protein tyrosine phosphatase (PTP) and two SH2 domains. Selective ... ...

Abstract	SHP2 is a phosphatase/adaptor protein that plays an important role in various signaling pathways. Its mutations are associated with cancers and developmental diseases. SHP2 contains a protein tyrosine phosphatase (PTP) and two SH2 domains. Selective inhibition of these domains has been challenging due to the multitude of homologous proteins in the proteome. Here, we developed a monobody, synthetic binding protein, that bound to and inhibited the SHP2 PTP domain. It was selective to SHP2 PTP over close homologs. A crystal structure of the monobody-PTP complex revealed that the monobody bound both highly conserved residues in the active site and less conserved residues in the periphery, rationalizing its high selectivity. Its epitope overlapped with the interface between the PTP and N-terminal SH2 domains that is formed in auto-inhibited SHP2. By using the monobody as a probe for the accessibility of the PTP active site, we developed a simple, nonenzymatic assay for the allosteric regulation of SHP2. The assay showed that, in the absence of an activating phospho-Tyr ligand, wild-type SHP2 and the "PTP-dead" C459E mutant were predominantly in the closed state in which the PTP active site is inaccessible, whereas the E76K and C459S mutants were in the open, active state. It also revealed that previously developed monobodies to the SH2 domains, ligands lacking a phospho-Tyr, weakly favored the open state. These results provide corroboration for a conformational equilibrium underlying allosteric regulation of SHP2, provide powerful tools for characterizing and controlling SHP2 functions, and inform drug discovery against SHP2.
MeSH term(s)	Humans ; Allosteric Regulation/drug effects ; Mutation ; Neoplasms/genetics ; Protein Tyrosine Phosphatase, Non-Receptor Type 11/antagonists & inhibitors ; Protein Tyrosine Phosphatase, Non-Receptor Type 11/chemistry ; Signal Transduction ; Protein Domains ; Enzyme Inhibitors/chemistry ; Enzyme Inhibitors/pharmacology ; Antineoplastic Agents/chemistry ; Antineoplastic Agents/pharmacology
Chemical Substances	Protein Tyrosine Phosphatase, Non-Receptor Type 11 (EC 3.1.3.48) ; Enzyme Inhibitors ; Antineoplastic Agents
Language	English
Publishing date	2023-02-16
Publishing country	Netherlands
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2023.168010
Database	MEDical Literature Analysis and Retrieval System OnLINE

Full text online

Accessible to users with ZB MED library card

In stock of ZB MED Cologne/Königswinter

Zs.A 867: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (1.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾

Article ; Online: Crystal structures of bacterial small multidrug resistance transporter EmrE in complex with structurally diverse substrates.

Kermani, Ali A / Burata, Olive E / Koff, B Ben / Koide, Akiko / Koide, Shohei / Stockbridge, Randy B

eLife

2022 Volume 11

Abstract: Proteins from the bacterial small multidrug resistance (SMR) family are proton-coupled exporters of diverse antiseptics and antimicrobials, including polyaromatic cations and quaternary ammonium compounds. The transport mechanism of ... ...

Abstract	Proteins from the bacterial small multidrug resistance (SMR) family are proton-coupled exporters of diverse antiseptics and antimicrobials, including polyaromatic cations and quaternary ammonium compounds. The transport mechanism of the
MeSH term(s)	Antiporters/metabolism ; Drug Resistance, Multiple ; Escherichia coli/metabolism ; Escherichia coli Proteins/metabolism ; Membrane Transport Proteins/metabolism
Chemical Substances	Antiporters ; Escherichia coli Proteins ; Membrane Transport Proteins ; EmrE protein, E coli (147995-06-0)
Language	English
Publishing date	2022-03-07
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.76766
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article ; Online: Monobodies as tool biologics for accelerating target validation and druggable site discovery.

Akkapeddi, Padma / Teng, Kai Wen / Koide, Shohei

RSC medicinal chemistry

2021 Volume 12, Issue 11, Page(s) 1839–1853

Abstract: Despite increased investment and technological advancement, new drug approvals have not proportionally increased. Low drug approval rates, particularly for new targets, are linked to insufficient target validation at early stages. Thus, there remains a ... ...

Abstract	Despite increased investment and technological advancement, new drug approvals have not proportionally increased. Low drug approval rates, particularly for new targets, are linked to insufficient target validation at early stages. Thus, there remains a strong need for effective target validation techniques. Here, we review the use of synthetic binding proteins as tools for drug target validation, with focus on the monobody platform among several advanced synthetic binding protein platforms. Monobodies with high affinity and high selectivity can be rapidly developed against challenging targets, such as KRAS mutants, using protein engineering technologies. They have strong tendency to bind to functional sites and thus serve as drug-like molecules, and they can serve as targeting ligands for constructing bio-PROTACs. Genetically encoded monobodies are effective "tool biologics" for validating intracellular targets. They promote crystallization and help reveal the atomic structures of the monobody-target interface, which can inform drug design. Using case studies, we illustrate the potential of the monobody technology in accelerating target validation and small-molecule drug discovery.
Language	English
Publishing date	2021-09-13
Publishing country	England
Document type	Journal Article ; Review
ISSN	2632-8682
ISSN (online)	2632-8682
DOI	10.1039/d1md00188d
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: Monobodies as enabling tools for structural and mechanistic biology.

Hantschel, Oliver / Biancalana, Matthew / Koide, Shohei

Current opinion in structural biology

2020 Volume 60, Page(s) 167–174

Abstract: Monobodies, built with the scaffold of the fibronectin type III domain, are among the most well-established synthetic binding proteins. They promote crystallization of challenging molecular systems. They have strong tendency to bind to functional sites ... ...

Abstract	Monobodies, built with the scaffold of the fibronectin type III domain, are among the most well-established synthetic binding proteins. They promote crystallization of challenging molecular systems. They have strong tendency to bind to functional sites and thus serve as drug-like molecules that perturb the biological functions of their targets. Monobodies lack disulfide bonds and thus they are particularly suited as genetically encoded reagents to be used intracellularly. This article reviews recent monobody-enabled studies that reveal new structures, molecular mechanisms and potential therapeutic opportunities. A systematic analysis of the crystal structures of monobody-target complexes suggests important attributes that make monobodies effective crystallization chaperones.
MeSH term(s)	Crystallography, X-Ray ; Fibronectins/chemistry ; Humans ; Protein Domains ; Single-Domain Antibodies/metabolism
Chemical Substances	Fibronectins ; Single-Domain Antibodies
Language	English
Publishing date	2020-03-04
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	1068353-7
ISSN	1879-033X ; 0959-440X
ISSN (online)	1879-033X
ISSN	0959-440X
DOI	10.1016/j.sbi.2020.01.015
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 3206: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (2.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: Rapid airway stenosis due to ruptured occipital artery in a patient with neurofibromatosis type I.

Ando, Hirotaka / Goto, Takeshi / Ito, Keisuke / Ikebe, Dai / Tanno, Shogo / Matsukubo, Shohei / Koide, Hirohumi / Abe, Toshikazu

Acute medicine & surgery

2023 Volume 10, Issue 1, Page(s) e832

Abstract: Background: Neurofibromatosis type I is rarely associated with vascular abnormalities. Here, we report a case of rapid airway stenosis caused by a ruptured occipital artery that was treated with surgical airway management.: Case presentation: A 40- ... ...

Abstract	Background: Neurofibromatosis type I is rarely associated with vascular abnormalities. Here, we report a case of rapid airway stenosis caused by a ruptured occipital artery that was treated with surgical airway management. Case presentation: A 40-year-old woman, with no medical history, presented with a chief complaint of a sudden neck pain on the left side. She had a prominent mass in the outer left side of the neck. After arrival at the emergency room, the patient complained of severe dyspnea and experienced a rapid drop in oxygen saturation. Supplemental ventilation was ineffective, and tracheal intubation was attempted; however, laryngeal expansion could not be observed because of the enlarged cervical mass. Therefore, to manage the surgical airway, a cricothyrotomy was first carried out, which resulted in an immediate increase in oxygen saturation. Two percutaneous embolizations and one surgical procedure were carried out, and the patient was discharged without any complications. Conclusion: For a sudden onset cervical mass, airway management should be undertaken, keeping in mind the possibility of worsening rapid airway narrowing due to bleeding.
Language	English
Publishing date	2023-04-09
Publishing country	United States
Document type	Case Reports
ZDB-ID	2751184-4
ISSN	2052-8817 ; 2052-8817
ISSN (online)	2052-8817
ISSN	2052-8817
DOI	10.1002/ams2.835
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article ; Online: Next-generation antibodies for post-translational modifications.

Hattori, Takamitsu / Koide, Shohei

Current opinion in structural biology

2018 Volume 51, Page(s) 141–148

Abstract: Despite increasing demands for antibodies to post-translational modifications (PTMs), fundamental difficulties in molecular recognition of PTMs hinder the generation of highly functional anti-PTM antibodies using conventional methods. Recently, advanced ... ...

Abstract	Despite increasing demands for antibodies to post-translational modifications (PTMs), fundamental difficulties in molecular recognition of PTMs hinder the generation of highly functional anti-PTM antibodies using conventional methods. Recently, advanced approaches in protein engineering and design that have been established for biologics development were applied to successfully generating highly functional anti-PTM antibodies. Furthermore, structural analyses of anti-PTM antibodies revealed unprecedented binding modes that substantially increased the antigen-binding surface. These features deepen the understanding of mechanisms underlying specific recognition of PTMs, which may lead to more effective approaches for generating anti-PTM antibodies with exquisite specificity and high affinity.
MeSH term(s)	Antibodies/chemistry ; Antibodies/metabolism ; Antibodies/pharmacology ; Drug Design ; Models, Molecular ; Protein Binding ; Protein Conformation ; Protein Engineering ; Protein Processing, Post-Translational/drug effects ; Structure-Activity Relationship
Chemical Substances	Antibodies
Language	English
Publishing date	2018-05-10
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Review
ZDB-ID	1068353-7
ISSN	1879-033X ; 0959-440X
ISSN (online)	1879-033X
ISSN	0959-440X
DOI	10.1016/j.sbi.2018.04.006
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 3206: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (2.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

To top

More links

Kategorien

Order via subito

Inter-library loan at ZB MED

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

Full text online

More links

Kategorien

Order via subito

Inter-library loan at ZB MED

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

Full text online

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

Order via subito

More links

Kategorien

Order via subito

Inter-library loan at ZB MED

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

Order via subito

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito