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Article ; Online: Rational design of humanized antibody inhibitors for cathepsin S.

Yu, Po-Wen / Kao, Guoyun / Dai, Zhefu / Nasertorabi, Fariborz / Zhang, Yong

2023 Volume 751, Page(s) 109849

Abstract: Cathepsin S (CTSS) is involved in pathogenesis of many human diseases. Inhibitors blocking its protease activity hold therapeutic potential. In comparison to small-molecule inhibitors, monoclonal antibodies capable of inhibiting CTSS enzymatic activity ... ...

Abstract	Cathepsin S (CTSS) is involved in pathogenesis of many human diseases. Inhibitors blocking its protease activity hold therapeutic potential. In comparison to small-molecule inhibitors, monoclonal antibodies capable of inhibiting CTSS enzymatic activity may possess advantageous pharmacological properties. Here we designed and produced inhibitory antibodies targeting human CTSS by genetically fusing the propeptide of procathepsin S (proCTSS) with antibodies in clinic. The resulting antibody fusions in full-length or fragment antigen-binding format could be stably expressed and potently inhibit CTSS proteolytic activity in high specificity. These fusion antibodies not only demonstrate a new approach for facile synthesis of antibody inhibitors against CTSS, but also represent novel anti-CTSS therapeutic candidates.
MeSH term(s)	Humans ; Antibodies, Monoclonal, Humanized/pharmacology ; Cathepsins/metabolism ; Proteolysis
Chemical Substances	Antibodies, Monoclonal, Humanized ; Cathepsins (EC 3.4.-)
Language	English
Publishing date	2023-12-05
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	523-x
ISSN	1096-0384 ; 0003-9861
ISSN (online)	1096-0384
ISSN	0003-9861
DOI	10.1016/j.abb.2023.109849
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Article ; Online: A Single Reactive Noncanonical Amino Acid is Able to Dramatically Stabilize Protein Structure.

Li, Jack C / Nasertorabi, Fariborz / Xuan, Weimin / Han, Gye Won / Stevens, Raymond C / Schultz, Peter G

ACS chemical biology

2020 Volume 15, Issue 10, Page(s) 2842

Language	English
Publishing date	2020-10-02
Publishing country	United States
Document type	Published Erratum
ISSN	1554-8937
ISSN (online)	1554-8937
DOI	10.1021/acschembio.0c00196
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Article ; Online: An orthogonal seryl-tRNA synthetase/tRNA pair for noncanonical amino acid mutagenesis in Escherichia coli.

Zambaldo, Claudio / Koh, Minseob / Nasertorabi, Fariborz / Han, Gye Won / Chatterjee, Abhishek / Stevens, Raymond C / Schultz, Peter G

Bioorganic & medicinal chemistry

2020 Volume 28, Issue 20, Page(s) 115662

Abstract: We report the development of the orthogonal amber-suppressor pair Archaeoglobus fulgidus seryl-tRNA (Af- ... ...

Abstract	We report the development of the orthogonal amber-suppressor pair Archaeoglobus fulgidus seryl-tRNA (Af-tRNA
MeSH term(s)	Amino Acids/genetics ; Amino Acids/metabolism ; Archaeoglobus fulgidus/enzymology ; Escherichia coli/metabolism ; Methanosarcina/enzymology ; Protein Engineering ; RNA, Transfer/chemistry ; RNA, Transfer/metabolism ; Serine-tRNA Ligase/chemistry ; Serine-tRNA Ligase/metabolism
Chemical Substances	Amino Acids ; RNA, Transfer (9014-25-9) ; Serine-tRNA Ligase (EC 6.1.1.11)
Language	English
Publishing date	2020-07-28
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	1161284-8
ISSN	1464-3391 ; 0968-0896
ISSN (online)	1464-3391
ISSN	0968-0896
DOI	10.1016/j.bmc.2020.115662
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Article: Generation of an Orthogonal ProteinâProtein Interface with a Noncanonical Amino Acid

Koh, Minseob / Han Gye Won / Nasertorabi Fariborz / Schultz Peter G / Stevens Raymond C

Journal of the American Chemical Society. 2017 Apr. 26, v. 139, no. 16

2017

Abstract: We have engineered the protein interface of the Escherichia coli chorismate mutase (EcCM) homodimer to be dependent on incorporation of a noncanonical amino acid (ncAA) at residue 72. The large hydrophobic amino acid p-benzoyl phenylalanine (pBzF) was ... ...

Abstract	We have engineered the protein interface of the Escherichia coli chorismate mutase (EcCM) homodimer to be dependent on incorporation of a noncanonical amino acid (ncAA) at residue 72. The large hydrophobic amino acid p-benzoyl phenylalanine (pBzF) was substituted for Tyr72, which led to a catalytically inactive protein. A library of five residues (Leu25â², Arg29â², Leu76, Ile80â² and Asp83â²) surrounding pBzF72 was generated and subjected to a growth based selection in a chorismate mutase deficient strain. An EcCM variant (Phe25â², pBzF72, Thr76, Gly80â² and Tyr83â²) forms a stable homodimer, has catalytic activity similar to the wild type enzyme, and unfolds with a Tâ of 53 Â°C. The X-ray crystal structure reveals a piâpi stacking and hydrogen bonding interactions that stabilize the new protein interface. The strategy described here should be useful for generating organisms that are dependent on the presence of a ncAA for growth.
Keywords	catalytic activity ; chorismic acid ; Escherichia coli ; hydrogen bonding ; hydrophobicity ; phenylalanine ; protein-protein interactions ; X-ray diffraction
Language	English
Dates of publication	2017-0426
Size	p. 5728-5731.
Publishing place	American Chemical Society
Document type	Article
ZDB-ID	3155-0
ISSN	1520-5126 ; 0002-7863
ISSN (online)	1520-5126
ISSN	0002-7863
DOI	10.1021%2Fjacs.7b02273
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Article ; Online: Generation of an Orthogonal Protein-Protein Interface with a Noncanonical Amino Acid.

Koh, Minseob / Nasertorabi, Fariborz / Han, Gye Won / Stevens, Raymond C / Schultz, Peter G

Journal of the American Chemical Society

2017 Volume 139, Issue 16, Page(s) 5728–5731

Abstract	We have engineered the protein interface of the Escherichia coli chorismate mutase (EcCM) homodimer to be dependent on incorporation of a noncanonical amino acid (ncAA) at residue 72. The large hydrophobic amino acid p-benzoyl phenylalanine (pBzF) was substituted for Tyr72, which led to a catalytically inactive protein. A library of five residues (Leu25', Arg29', Leu76, Ile80' and Asp83') surrounding pBzF72 was generated and subjected to a growth based selection in a chorismate mutase deficient strain. An EcCM variant (Phe25', pBzF72, Thr76, Gly80' and Tyr83') forms a stable homodimer, has catalytic activity similar to the wild type enzyme, and unfolds with a T
Language	English
Publishing date	2017-04-26
Publishing country	United States
Document type	Journal Article
ZDB-ID	3155-0
ISSN	1520-5126 ; 0002-7863
ISSN (online)	1520-5126
ISSN	0002-7863
DOI	10.1021/jacs.7b02273
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Article: Facile chemoenzymatic synthesis of a novel stable mimic of NAD

Dai, Zhefu / Zhang, Xiao-Nan / Nasertorabi, Fariborz / Cheng, Qinqin / Pei, Hua / Louie, Stan G / Stevens, Raymond C / Zhang, Yong

Chemical science

2018 Volume 9, Issue 44, Page(s) 8337–8342

Abstract: Nicotinamide adenine dinucleotide ( ... ...

Abstract	Nicotinamide adenine dinucleotide (NAD
Language	English
Publishing date	2018-10-15
Publishing country	England
Document type	Journal Article
ZDB-ID	2559110-1
ISSN	2041-6539 ; 2041-6520
ISSN (online)	2041-6539
ISSN	2041-6520
DOI	10.1039/c8sc03899f
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Article ; Online: Synthesis of site-specific antibody-drug conjugates by ADP-ribosyl cyclases.

Dai, Zhefu / Zhang, Xiao-Nan / Nasertorabi, Fariborz / Cheng, Qinqin / Li, Jiawei / Katz, Benjamin B / Smbatyan, Goar / Pei, Hua / Louie, Stan G / Lenz, Heinz-Josef / Stevens, Raymond C / Zhang, Yong

Science advances

2020 Volume 6, Issue 23, Page(s) eaba6752

Abstract: Most of the current antibody-drug conjugates (ADCs) in clinic are heterogeneous mixtures. To produce homogeneous ADCs, established procedures often require multiple steps or long reaction times. The introduced mutations or foreign sequences may cause ... ...

Abstract	Most of the current antibody-drug conjugates (ADCs) in clinic are heterogeneous mixtures. To produce homogeneous ADCs, established procedures often require multiple steps or long reaction times. The introduced mutations or foreign sequences may cause high immunogenicity. Here, we explore a new concept of transforming CD38 enzymatic activity into a facile approach for generating site-specific ADCs. This was achieved through coupling bifunctional antibody-CD38 fusion proteins with designer dinucleotide-based covalent inhibitors with stably attached payloads. The resulting adenosine diphosphate-ribosyl cyclase-enabled ADC (ARC-ADC) with a drug-to-antibody ratio of 2 could be rapidly generated through single-step conjugation. The generated ARC-ADC targeting human epidermal growth factor receptor 2 (HER2) displays excellent stability and potency against HER2-positive breast cancer both in vitro and in vivo. This proof-of-concept study demonstrates a new strategy for production of site-specific ADCs. It may provide a general approach for the development of a novel class of ADCs with potentially enhanced properties.
MeSH term(s)	ADP-ribosyl Cyclase/therapeutic use ; Antineoplastic Agents/pharmacology ; Antineoplastic Agents/therapeutic use ; Breast Neoplasms/metabolism ; Female ; Humans ; Immunoconjugates/pharmacology
Chemical Substances	Antineoplastic Agents ; Immunoconjugates ; ADP-ribosyl Cyclase (EC 3.2.2.5)
Language	English
Publishing date	2020-06-03
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2810933-8
ISSN	2375-2548 ; 2375-2548
ISSN (online)	2375-2548
ISSN	2375-2548
DOI	10.1126/sciadv.aba6752
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Article ; Online: Insights into the structure of the CCR4-NOT complex by electron microscopy.

Nasertorabi, Fariborz / Batisse, Claire / Diepholz, Meikel / Suck, Dietrich / Böttcher, Bettina

FEBS letters

2011 Volume 585, Issue 14, Page(s) 2182–2186

Abstract: The CCR4-NOT complex is a deadenylation complex, which plays a major role for mRNA stability. The complex is conserved from yeast to human and consists of nine proteins NOT1-NOT5, CCR4, CAF1, CAF40 and CAF130. We have successfully isolated the complex ... ...

Abstract	The CCR4-NOT complex is a deadenylation complex, which plays a major role for mRNA stability. The complex is conserved from yeast to human and consists of nine proteins NOT1-NOT5, CCR4, CAF1, CAF40 and CAF130. We have successfully isolated the complex using a Protein A tag on NOT1, followed by cross-linking on a glycerol gradient. All components of the complex were identified by mass spectrometry. Electron microscopy of negatively stained particles followed by image reconstruction revealed an L-shaped complex with two arms of similar length. The arms form an accessible cavity, which we think could provide an extensive interface for RNA-deadenylation.
MeSH term(s)	Cell Cycle Proteins/genetics ; Cell Cycle Proteins/isolation & purification ; Cell Cycle Proteins/ultrastructure ; Humans ; Mass Spectrometry/methods ; Microscopy, Electron/methods ; Models, Molecular ; Multiprotein Complexes/chemistry ; Multiprotein Complexes/isolation & purification ; Protein Subunits/chemistry ; Protein Subunits/genetics ; Protein Subunits/isolation & purification ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; Ribonucleases/genetics ; Ribonucleases/isolation & purification ; Ribonucleases/ultrastructure ; Saccharomyces cerevisiae/chemistry ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/isolation & purification ; Saccharomyces cerevisiae Proteins/ultrastructure ; Transcription Factors/genetics ; Transcription Factors/isolation & purification ; Transcription Factors/ultrastructure
Chemical Substances	CDC39 protein, S cerevisiae ; Cell Cycle Proteins ; Multiprotein Complexes ; Protein Subunits ; RNA, Messenger ; Saccharomyces cerevisiae Proteins ; Transcription Factors ; CCR4 protein, S cerevisiae (EC 3.1.-) ; Ribonucleases (EC 3.1.-) ; POP2 protein, S cerevisiae (EC 3.1.13.4)
Language	English
Publishing date	2011-06-12
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	212746-5
ISSN	1873-3468 ; 0014-5793
ISSN (online)	1873-3468
ISSN	0014-5793
DOI	10.1016/j.febslet.2011.05.071
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Article: Insights into the structure of the CCR4-NOT complex by electron microscopy

Nasertorabi, Fariborz / Batisse, Claire / Diepholz, Meikel / Suck, Dietrich / Böttcher, Bettina

FEBS letters. 2011 July 21, v. 585, no. 14

2011

Abstract: The CCR4-NOT complex is a deadenylation complex, which plays a major role for mRNA stability. The complex is conserved from yeast to human and consists of nine proteins NOT1–NOT5, CCR4, CAF1, CAF40 and CAF130. We have successfully isolated the complex ... ...

Abstract	The CCR4-NOT complex is a deadenylation complex, which plays a major role for mRNA stability. The complex is conserved from yeast to human and consists of nine proteins NOT1–NOT5, CCR4, CAF1, CAF40 and CAF130. We have successfully isolated the complex using a Protein A tag on NOT1, followed by cross-linking on a glycerol gradient. All components of the complex were identified by mass spectrometry. Electron microscopy of negatively stained particles followed by image reconstruction revealed an L-shaped complex with two arms of similar length. The arms form an accessible cavity, which we think could provide an extensive interface for RNA-deadenylation. STRUCTURED SUMMARY OF PROTEIN INTERACTIONS: CAF1physically interactswithCCR4 and NOT1 by tandem affinity purification(View interaction)
Keywords	CCR4 receptor ; crosslinking ; electron microscopy ; glycerol ; humans ; mass spectrometry ; messenger RNA ; yeasts
Language	English
Dates of publication	2011-0721
Size	p. 2182-2186.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	212746-5
ISSN	1873-3468 ; 0014-5793
ISSN (online)	1873-3468
ISSN	0014-5793
DOI	10.1016/j.febslet.2011.05.071
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Article ; Online: Distinctive Structure of the EphA3/Ephrin-A5 Complex Reveals a Dual Mode of Eph Receptor Interaction for Ephrin-A5.

Forse, Garry Jason / Uson, Maria Loressa / Nasertorabi, Fariborz / Kolatkar, Anand / Lamberto, Ilaria / Pasquale, Elena Bianca / Kuhn, Peter

PloS one

2015 Volume 10, Issue 5, Page(s) e0127081

Abstract: The Eph receptor tyrosine kinase/ephrin ligand system regulates a wide spectrum of physiological processes, while its dysregulation has been implicated in cancer progression. The human EphA3 receptor is widely upregulated in the tumor microenvironment ... ...

Abstract	The Eph receptor tyrosine kinase/ephrin ligand system regulates a wide spectrum of physiological processes, while its dysregulation has been implicated in cancer progression. The human EphA3 receptor is widely upregulated in the tumor microenvironment and is highly expressed in some types of cancer cells. Furthermore, EphA3 is among the most highly mutated genes in lung cancer and it is also frequently mutated in other cancers. We report the structure of the ligand-binding domain of the EphA3 receptor in complex with its preferred ligand, ephrin-A5. The structure of the complex reveals a pronounced tilt of the ephrin-A5 ligand compared to its orientation when bound to the EphA2 and EphB2 receptors and similar to its orientation when bound to EphA4. This tilt brings an additional area of ephrin-A5 into contact with regions of EphA3 outside the ephrin-binding pocket thereby enlarging the size of the interface, which is consistent with the high binding affinity of ephrin-A5 for EphA3. This large variation in the tilt of ephrin-A5 bound to different Eph receptors has not been previously observed for other ephrins.
MeSH term(s)	Binding Sites ; Calorimetry ; Crystallography, X-Ray ; Ephrin-A5/chemistry ; Ephrin-A5/metabolism ; Humans ; Models, Molecular ; Protein Binding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Receptor, EphA3/chemistry ; Receptor, EphA3/metabolism ; Surface Properties ; Thermodynamics
Chemical Substances	Ephrin-A5 ; Receptor, EphA3 (EC 2.7.10.1)
Language	English
Publishing date	2015
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0127081
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