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Article ; Online: YESS 2.0, a Tunable Platform for Enzyme Evolution, Yields Highly Active TEV Protease Variants.

Denard, Carl A / Paresi, Chelsea / Yaghi, Rasha / McGinnis, Natalie / Bennett, Zachary / Yi, Li / Georgiou, George / Iverson, Brent L

ACS synthetic biology

2021 Volume 10, Issue 1, Page(s) 63–71

Abstract: Here we describe YESS 2.0, a highly versatile version of the yeast endoplasmic sequestration screening (YESS) system suitable for engineering and characterizing protein/peptide modifying enzymes such as proteases with desired new activities. By ... ...

Abstract	Here we describe YESS 2.0, a highly versatile version of the yeast endoplasmic sequestration screening (YESS) system suitable for engineering and characterizing protein/peptide modifying enzymes such as proteases with desired new activities. By incorporating features that modulate gene transcription as well as substrate and enzyme spatial sequestration, YESS 2.0 achieves a significantly higher operational and dynamic range compared with the original YESS. To showcase the new advantages of YESS 2.0, we improved an already efficient TEV protease variant (TEV-EAV) to obtain a variant (eTEV) with a 2.25-fold higher catalytic efficiency, derived almost entirely from an increase in turnover rate (
MeSH term(s)	Amino Acid Sequence ; Biocatalysis ; Endopeptidases/genetics ; Endopeptidases/metabolism ; Evolution, Molecular ; Kinetics ; Metabolic Engineering ; Mutagenesis, Site-Directed ; Peptides/chemistry ; Peptides/metabolism ; Plasmids/genetics ; Plasmids/metabolism ; Saccharomyces cerevisiae/metabolism ; Substrate Specificity
Chemical Substances	Peptides ; Endopeptidases (EC 3.4.-) ; TEV protease (EC 3.4.-)
Language	English
Publishing date	2021-01-05
Publishing country	United States
Document type	Journal Article
ISSN	2161-5063
ISSN (online)	2161-5063
DOI	10.1021/acssynbio.0c00452
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Benzimidazole covalent probes and the gastric H(+)/K(+)-ATPase as a model system for protein labeling in a copper-free setting.

Paresi, Chelsea J / Liu, Qi / Li, Yue-Ming

Molecular bioSystems

2016 Volume 12, Issue 6, Page(s) 1772–1780

Abstract: Affinity probes are useful tools for determining molecular targets and elucidating mechanism of action for novel, bioactive compounds. In the case of covalent inhibitors, activity based probes are particularly valuable for ensuring acceptable selectivity ...

Abstract	Affinity probes are useful tools for determining molecular targets and elucidating mechanism of action for novel, bioactive compounds. In the case of covalent inhibitors, activity based probes are particularly valuable for ensuring acceptable selectivity margins. However, there is a variety of bioorthogonal chemistry reactions available for modifying compounds of interest with clickable tags. Here, we describe a direct comparison of tetrazine ligation and strain promoted azide-alkyne cycloaddition using benzimidazole based probes to bind their known target, the gastric proton pump, ATP4A. This study validates the use of chemical probes for target identification and illustrates the superior efficiency of tetrazine ligation for copper-free click systems. In addition, we have identified several novel binding partners of benzimidazole probes: Isoform 2 of deleted in malignant brain tumors 1 protein (DMBT1) and three uncharacterized proteins.
MeSH term(s)	Benzimidazoles/chemical synthesis ; Benzimidazoles/chemistry ; Copper/chemistry ; Fluorescent Dyes/chemistry ; H(+)-K(+)-Exchanging ATPase/chemistry ; H(+)-K(+)-Exchanging ATPase/metabolism ; Mass Spectrometry ; Microscopy, Fluorescence ; Molecular Probes/chemical synthesis ; Molecular Probes/chemistry ; Molecular Structure ; Proton Pump Inhibitors/chemical synthesis ; Proton Pump Inhibitors/chemistry ; Staining and Labeling
Chemical Substances	Benzimidazoles ; Fluorescent Dyes ; Molecular Probes ; Proton Pump Inhibitors ; Copper (789U1901C5) ; benzimidazole (E24GX49LD8) ; H(+)-K(+)-Exchanging ATPase (EC 3.6.3.10)
Language	English
Publishing date	2016-05
Publishing country	England
Document type	Journal Article
ZDB-ID	2188635-0
ISSN	1742-2051 ; 1742-206X
ISSN (online)	1742-2051
ISSN	1742-206X
DOI	10.1039/c6mb00024j
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Hybrid immunity to SARS-CoV-2 arises from serological recall of IgG antibodies distinctly imprinted by infection or vaccination.

Voss, William N / Mallory, Michael A / Byrne, Patrick O / Marchioni, Jeffrey M / Knudson, Sean A / Powers, John M / Leist, Sarah R / Dadonaite, Bernadeta / Townsend, Douglas R / Kain, Jessica / Huang, Yimin / Satterwhite, Ed / Castillo, Izabella N / Mattocks, Melissa / Paresi, Chelsea / Munt, Jennifer E / Scobey, Trevor / Seeger, Allison / Premkumar, Lakshmanane /

Bloom, Jesse D / Georgiou, George / McLellan, Jason S / Baric, Ralph S / Lavinder, Jason J / Ippolito, Gregory C

bioRxiv : the preprint server for biology

2024

Abstract: We used plasma IgG proteomics to study the molecular composition and temporal durability of polyclonal IgG antibodies triggered by ancestral SARS-CoV-2 infection, vaccination, or their combination ("hybrid immunity"). Infection, whether primary or post- ... ...

Abstract	We used plasma IgG proteomics to study the molecular composition and temporal durability of polyclonal IgG antibodies triggered by ancestral SARS-CoV-2 infection, vaccination, or their combination ("hybrid immunity"). Infection, whether primary or post-vaccination, mainly triggered an anti-spike antibody response to the S2 domain, while vaccination predominantly induced anti-RBD antibodies. Immunological imprinting persisted after a secondary (hybrid) exposure, with >60% of the ensuing serological response originating from the initial antibodies generated during the first exposure. We highlight one instance where hybrid immunity arising from breakthrough infection resulted in a marked increase in the breadth and affinity of a highly abundant vaccination-elicited plasma IgG antibody, SC27. With an intrinsic binding affinity surpassing a theoretical maximum (K Highlights: ▪ Infection and vaccination elicit unique IgG antibody profiles at the molecular level▪ Immunological imprinting varies between infection (S2/NTD) and vaccination (RBD)▪ Hybrid immunity maintains the imprint of first infection or first vaccination▪ Hybrid immune IgG plasma mAbs have superior neutralization potency and breadth.
Language	English
Publishing date	2024-01-23
Publishing country	United States
Document type	Preprint
DOI	10.1101/2024.01.22.576742
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Article ; Online: Chemical synthesis of the ATAD2 bromodomain.

Creech, Gardner S / Paresi, Chelsea / Li, Yue-Ming / Danishefsky, Samuel J

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

2014 Volume 111, Issue 8, Page(s) 2891–2896

Abstract: Due to the emerging importance of the bromodomain binding region in the study of epigenetic effectors and the vast implications for a wide variety of human disease, the bromodomain region of human ATPase family AAA+ (ATPases associated with diverse ... ...

Abstract	Due to the emerging importance of the bromodomain binding region in the study of epigenetic effectors and the vast implications for a wide variety of human disease, the bromodomain region of human ATPase family AAA+ (ATPases associated with diverse cellular activities) domain-containing protein 2 (ATAD2) was targeted for chemical synthesis. The ATAD2 bromodomain (130 aa) was divided into five strategic fragments to be assembled using native chemical ligation with a focus on maximal convergency and efficiency. The fragments were assembled with one cysteine and three thioleucine ligations, unveiling the native alanine and leucine amino acids at the ligation points following metal-free dethiylation. Synthetic highlights of the study are a photolabile dimethoxynitrobenzyl-protected glutamic acid side chain used to impede hydrolysis of the C-terminal Glu-thioester, a thiazolidine-protected thioleucine, and an efficient assembly of three fragments in a single reaction vessel with dual-mode kinetic-standard chemical ligation. With a focus on material throughput and convergency, the five peptide fragments were assembled into the native ATAD2 bromodomain region with a total of three HPLC events in 8% overall yield from the fragments.
MeSH term(s)	ATPases Associated with Diverse Cellular Activities ; Adenosine Triphosphatases/chemical synthesis ; Chromatography, High Pressure Liquid ; DNA-Binding Proteins/chemical synthesis ; Humans ; Magnetic Resonance Spectroscopy ; Mass Spectrometry ; Peptide Fragments/chemistry ; Protein Structure, Tertiary ; Solid-Phase Synthesis Techniques/methods
Chemical Substances	DNA-Binding Proteins ; Peptide Fragments ; Adenosine Triphosphatases (EC 3.6.1.-) ; ATAD2 protein, human (EC 3.6.1.3) ; ATPases Associated with Diverse Cellular Activities (EC 3.6.4.-)
Language	English
Publishing date	2014-02-10
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.1400556111
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Zs.A 1148: Show issues

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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)

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Article ; Online: γ-Secretase Partitioning into Lipid Bilayers Remodels Membrane Microdomains after Direct Insertion.

Barros, Marilia / Houlihan, William J / Paresi, Chelsea J / Brendel, Matthew / Rynearson, Kevin D / Lee, Chang-Wook / Prikhodko, Olga / Cregger, Cristina / Chang, Geoffrey / Wagner, Steven L / Gilchrist, M Lane / Li, Yue-Ming

Langmuir : the ACS journal of surfaces and colloids

2020 Volume 36, Issue 23, Page(s) 6569–6579

Abstract: γ-Secretase is a multisubunit complex that catalyzes intramembranous cleavage of transmembrane proteins. The lipid environment forms membrane microdomains that serve as spatio-temporal platforms for proteins to function properly. Despite substantial ... ...

Abstract	γ-Secretase is a multisubunit complex that catalyzes intramembranous cleavage of transmembrane proteins. The lipid environment forms membrane microdomains that serve as spatio-temporal platforms for proteins to function properly. Despite substantial advances in the regulation of γ-secretase, the effect of the local membrane lipid microenvironment on the regulation of γ-secretase is poorly understood. Here, we characterized and quantified the partitioning of γ-secretase and its substrates, the amyloid precursor protein (APP) and Notch, into lipid bilayers using solid-supported model membranes. Notch substrate is preferentially localized in the liquid-disordered (L
MeSH term(s)	Amyloid Precursor Protein Secretases ; Amyloid beta-Protein Precursor ; Lipid Bilayers ; Membrane Lipids ; Membrane Microdomains
Chemical Substances	Amyloid beta-Protein Precursor ; Lipid Bilayers ; Membrane Lipids ; Amyloid Precursor Protein Secretases (EC 3.4.-)
Language	English
Publishing date	2020-06-04
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2005937-1
ISSN	1520-5827 ; 0743-7463
ISSN (online)	1520-5827
ISSN	0743-7463
DOI	10.1021/acs.langmuir.0c01178
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Article ; Online: Hybrid immunity to SARS-CoV-2 arises from serological recall of IgG antibodies distinctly imprinted by infection or vaccination

Voss, William N. / Mallory, Michael A. / Byrne, Patrick O. / Marchioni, Jeffrey M. / Knudson, Sean A. / Powers, John M. / Leist, Sarah R. / Dadonaite, Bernadeta / Townsend, Douglas R. / Kain, Jessica / Huang, Yimin / Satterwhite, Ed / Castillo, Izabella N. / Mattocks, Melissa / Paresi, Chelsea / Munt, Jennifer E. / Scobey, Trevor / Seeger, Allison / Premkumar, Lakshmanane /

Bloom, Jesse D. / Georgiou, George / McLellan, Jason S. / Baric, Ralph S. / Lavinder, Jason J. / Ippolito, Gregory C.

bioRxiv

Abstract	We used plasma IgG proteomics to study the molecular composition and temporal durability of polyclonal IgG antibodies triggered by ancestral SARS-CoV-2 infection, vaccination, or their combination ("hybrid immunity"). Infection, whether primary or post-vaccination, mainly triggered an anti-spike antibody response to the S2 domain, while vaccination predominantly induced anti-RBD antibodies. Immunological imprinting persisted after a secondary (hybrid) exposure, with >60% of the ensuing serological response originating from the initial antibodies generated during the first exposure. We highlight one instance where hybrid immunity arising from breakthrough infection resulted in a marked increase in the breadth and affinity of a highly abundant vaccination-elicited plasma IgG antibody, SC27. With an intrinsic binding affinity surpassing a theoretical maximum (K<sub>D</sub> < 5 pM), SC27 demonstrated potent neutralization of various SARS-CoV-2 variants and SARS-like zoonotic viruses (IC<sub>50</sub> ~0.1–1.75 nM) and provided robust protection in vivo. Cryo-EM structural analysis unveiled that SC27 binds to the RBD class 1/4 epitope, with both VH and VL significantly contributing to the binding interface. These findings suggest that exceptionally broad and potent antibodies can be prevalent in plasma and can largely dictate the nature of serological neutralization.
Keywords	covid19
Language	English
Publishing date	2024-01-23
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2024.01.22.576742
Database	COVID19

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Article: Prevalent, protective, and convergent IgG recognition of SARS-CoV-2 non-RBD spike epitopes in COVID-19 convalescent plasma.

Voss, William N / Hou, Yixuan J / Johnson, Nicole V / Kim, Jin Eyun / Delidakis, George / Horton, Andrew P / Bartzoka, Foteini / Paresi, Chelsea J / Tanno, Yuri / Abbasi, Shawn A / Pickens, Whitney / George, Katia / Boutz, Daniel R / Towers, Dalton M / McDaniel, Jonathan R / Billick, Daniel / Goike, Jule / Rowe, Lori / Batra, Dhwani /

Pohl, Jan / Lee, Justin / Gangappa, Shivaprakash / Sambhara, Suryaprakash / Gadush, Michelle / Wang, Nianshuang / Person, Maria D / Iverson, Brent L / Gollihar, Jimmy D / Dye, John / Herbert, Andrew / Baric, Ralph S / McLellan, Jason S / Georgiou, George / Lavinder, Jason J / Ippolito, Gregory C

bioRxiv : the preprint server for biology

2020

Abstract: Although humoral immunity is essential for control of SARS-CoV-2, the molecular composition, binding epitopes and effector functions of the immunoglobulin G (IgG) antibodies that circulate in blood plasma following infection are unknown. Proteomic ... ...

Abstract	Although humoral immunity is essential for control of SARS-CoV-2, the molecular composition, binding epitopes and effector functions of the immunoglobulin G (IgG) antibodies that circulate in blood plasma following infection are unknown. Proteomic deconvolution of the circulating IgG repertoire (Ig-Seq
Language	English
Publishing date	2020-12-21
Publishing country	United States
Document type	Preprint
DOI	10.1101/2020.12.20.423708
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Article ; Online: Prevalent, protective, and convergent IgG recognition of SARS-CoV-2 non-RBD spike epitopes.

Voss, William N / Hou, Yixuan J / Johnson, Nicole V / Delidakis, George / Kim, Jin Eyun / Javanmardi, Kamyab / Horton, Andrew P / Bartzoka, Foteini / Paresi, Chelsea J / Tanno, Yuri / Chou, Chia-Wei / Abbasi, Shawn A / Pickens, Whitney / George, Katia / Boutz, Daniel R / Towers, Dalton M / McDaniel, Jonathan R / Billick, Daniel / Goike, Jule /

Rowe, Lori / Batra, Dhwani / Pohl, Jan / Lee, Justin / Gangappa, Shivaprakash / Sambhara, Suryaprakash / Gadush, Michelle / Wang, Nianshuang / Person, Maria D / Iverson, Brent L / Gollihar, Jimmy D / Dye, John M / Herbert, Andrew S / Finkelstein, Ilya J / Baric, Ralph S / McLellan, Jason S / Georgiou, George / Lavinder, Jason J / Ippolito, Gregory C

Science (New York, N.Y.)

2021 Volume 372, Issue 6546, Page(s) 1108–1112

Abstract: The molecular composition and binding epitopes of the immunoglobulin G (IgG) antibodies that circulate in blood plasma after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection are unknown. Proteomic deconvolution of the IgG repertoire ...

Abstract	The molecular composition and binding epitopes of the immunoglobulin G (IgG) antibodies that circulate in blood plasma after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection are unknown. Proteomic deconvolution of the IgG repertoire to the spike glycoprotein in convalescent subjects revealed that the response is directed predominantly (>80%) against epitopes residing outside the receptor binding domain (RBD). In one subject, just four IgG lineages accounted for 93.5% of the response, including an amino (N)-terminal domain (NTD)-directed antibody that was protective against lethal viral challenge. Genetic, structural, and functional characterization of a multidonor class of "public" antibodies revealed an NTD epitope that is recurrently mutated among emerging SARS-CoV-2 variants of concern. These data show that "public" NTD-directed and other non-RBD plasma antibodies are prevalent and have implications for SARS-CoV-2 protection and antibody escape.
MeSH term(s)	Animals ; Antibodies, Monoclonal/blood ; Antibodies, Monoclonal/chemistry ; Antibodies, Monoclonal/immunology ; Antibodies, Neutralizing/blood ; Antibodies, Neutralizing/chemistry ; Antibodies, Neutralizing/immunology ; Antibodies, Viral/blood ; Antibodies, Viral/chemistry ; Antibodies, Viral/immunology ; Antibody Affinity ; COVID-19/immunology ; COVID-19/prevention & control ; Epitopes/immunology ; Humans ; Immune Evasion ; Immunoglobulin G/blood ; Immunoglobulin G/chemistry ; Immunoglobulin G/immunology ; Immunoglobulin Heavy Chains/immunology ; Immunoglobulin Variable Region/immunology ; Mice ; Mice, Inbred BALB C ; Mutation ; Protein Domains ; Proteomics ; SARS-CoV-2/genetics ; SARS-CoV-2/immunology ; Spike Glycoprotein, Coronavirus/chemistry ; Spike Glycoprotein, Coronavirus/genetics ; Spike Glycoprotein, Coronavirus/immunology
Chemical Substances	Antibodies, Monoclonal ; Antibodies, Neutralizing ; Antibodies, Viral ; Epitopes ; Immunoglobulin G ; Immunoglobulin Heavy Chains ; Immunoglobulin Variable Region ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2
Language	English
Publishing date	2021-05-04
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	128410-1
ISSN	1095-9203 ; 0036-8075
ISSN (online)	1095-9203
ISSN	0036-8075
DOI	10.1126/science.abg5268
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Zs.A 27: 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)
Zs.MG 77: Show issues

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Article ; Online: Prevalent, protective, and convergent IgG recognition of SARS-CoV-2 non-RBD spike epitopes in COVID-19 convalescent plasma

bioRxiv

Abstract	Although humoral immunity is essential for control of SARS-CoV-2, the molecular composition, binding epitopes and effector functions of the immunoglobulin G (IgG) antibodies that circulate in blood plasma following infection are unknown. Proteomic deconvolution of the circulating IgG repertoire (Ig-Seq) to the spike ectodomain (S-ECD) in four convalescent study subjects revealed that the plasma response is oligoclonal and directed predominantly (>80%) to S-ECD epitopes that lie outside the receptor binding domain (RBD). When comparing antibodies directed to either the RBD, the N-terminal domain (NTD) or the S2 subunit (S2) in one subject, just four IgG lineages (1 anti-S2, 2 anti-NTD and 1 anti-RBD) accounted for 93.5% of the repertoire. Although the anti-RBD and one of the anti-NTD antibodies were equally potently neutralizing in vitro, we nonetheless found that the anti-NTD antibody was sufficient for protection to lethal viral challenge, either alone or in combination as a cocktail where it dominated the effect of the other plasma antibodies. We identified in vivo protective plasma anti-NTD antibodies in 3/4 subjects analyzed and discovered a shared class of antibodies targeting the NTD that utilize unmutated or near-germline IGHV1-24, the most electronegative IGHV gene in the human genome. Structural analysis revealed that binding to NTD is dominated by interactions with the heavy chain, accounting for 89% of the entire interfacial area, with germline residues uniquely encoded by IGHV1-24 contributing 20% (149 Å<sup>2</sup>). Together with recent reports of germline IGHV1-24 antibodies isolated by B-cell cloning our data reveal a class of shared IgG antibodies that are readily observed in convalescent plasma and underscore the role of NTD-directed antibodies in protection against SARS-CoV-2 infection.
Keywords	covid19
Language	English
Publishing date	2020-12-21
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2020.12.20.423708
Database	COVID19

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