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Book: Peptide self-assembly

Nilsson, Bradley L. / Doran, Todd M.

methods and protocols

(Methods in molecular biology ; 1777 ; Springer protocols)

2018

Author's details	edited by Bradley L. Nilsson, Todd M. Doran
Series title	Methods in molecular biology ; 1777 Springer protocols
Collection
Keywords	protein self-assembly phenomena ; extracellular matrix proteins ; amyloid pathologies ; solid-state NMR ; spectroscopic
Subject code	570
Language	English
Size	xv, 452 Seiten, Illustrationen, Diagramme, 25.4 cm x 17.8 cm
Publisher	Humana Press
Publishing place	New York, NY
Publishing country	United States
Document type	Book
HBZ-ID	HT019702048
ISBN	978-1-4939-7809-0 ; 1-4939-7809-8 ; 9781493978113 ; 149397811X
Database	Catalogue ZB MED Medicine, Health

In stock of ZB MED Cologne/Königswinter

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Zs A 7042 -1777-	verfügbar in Königswinter	Königswinter

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Article ; Online: Photocaged dicarbonyl probe provides spatiotemporal control over protein glycation.

Hurben, Alexander K / Ge, Peng / Bouchard, Jacob L / Doran, Todd M / Tretyakova, Natalia Y

Chemical communications (Cambridge, England)

2022 Volume 58, Issue 6, Page(s) 855–858

Abstract: Protein glycation is a disease associated, non-enzymatic, posttranslational modification generated by endogenous dicarbonyl metabolites. Currently, there is a lack of chemical tools capable of studying protein adducts caused by this class of reactive ... ...

Abstract	Protein glycation is a disease associated, non-enzymatic, posttranslational modification generated by endogenous dicarbonyl metabolites. Currently, there is a lack of chemical tools capable of studying protein adducts caused by this class of reactive species. Here, we report a chemical biology platform, termed T-DiP (targetable-dicarbonyl precursor), that releases a physiologically relevant dose of bio-orthogonally functionalized dicarbonyl probe upon irradiation with 365 nm light. This approach enables protein glycation to be controlled with spatiotemporal precision within live cells and expands the chemical toolbox needed to elucidate the roles of glycated proteins across various pathologies.
MeSH term(s)	Cell Survival/drug effects ; Glycation End Products, Advanced/chemistry ; Glycation End Products, Advanced/metabolism ; Glycosylation ; HEK293 Cells ; Humans ; Ketones/chemistry ; Light ; Molecular Probes/chemistry ; Molecular Probes/metabolism ; Molecular Probes/pharmacology ; Proteins/chemistry ; Proteins/metabolism ; Pyruvaldehyde/chemistry
Chemical Substances	Glycation End Products, Advanced ; Ketones ; Molecular Probes ; Proteins ; Pyruvaldehyde (722KLD7415)
Language	English
Publishing date	2022-01-18
Publishing country	England
Document type	Journal Article
ZDB-ID	1472881-3
ISSN	1364-548X ; 1359-7345 ; 0009-241X
ISSN (online)	1364-548X
ISSN	1359-7345 ; 0009-241X
DOI	10.1039/d1cc06651j
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Article ; Online: Incorporation of an Azobenzene β-Turn Peptidomimetic into Amyloid-β to Probe Potential Structural Motifs Leading to β-Sheet Self-Assembly.

Doran, Todd M / Nilsson, Bradley L

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

2018 Volume 1777, Page(s) 387–406

Abstract: Alzheimer's disease (AD) is characterized by chronic neurodegeneration and the insidious accumulation of senile plaques comprised of the amyloid-β (Aβ) peptide. An important goal in AD research is to characterize the structural basis for how Aβ ... ...

Abstract	Alzheimer's disease (AD) is characterized by chronic neurodegeneration and the insidious accumulation of senile plaques comprised of the amyloid-β (Aβ) peptide. An important goal in AD research is to characterize the structural basis for how Aβ aggregates exert their noxious effects on neurons. We describe herein synthetic steps to incorporate a light-controlled β-turn mimetic, 3-(3-aminomethylphenylazo)-phenylacetic acid (AMPP), into the backbone of a putative turn region within Aβ. AMPP adopts a rigid β-hairpin turn when azobenzene is in the cis conformation, and can adopt an extended "β-arc" turn in the trans-azobenzene conformation. The long lifetimes of these conformationally stable isomers permit detailed biochemical analyses that help to clarify the controversial role played by these two types of turns during the toxic misfolding pathway of Aβ. Methods to photo-nucleate the cis- or trans-AMPP isomeric turns in aqueous buffer are also described. Finally, we detail selected techniques to characterize the Aβ aggregates derived from these photoisomerized variants.
MeSH term(s)	Alzheimer Disease ; Amino Acid Motifs ; Amyloid beta-Peptides/chemical synthesis ; Amyloid beta-Peptides/chemistry ; Amyloid beta-Peptides/isolation & purification ; Amyloid beta-Peptides/ultrastructure ; Azo Compounds/chemistry ; Buffers ; Isomerism ; Molecular Conformation ; Molecular Structure ; Peptides/chemical synthesis ; Peptides/chemistry ; Peptides/isolation & purification ; Protein Aggregates ; Protein Aggregation, Pathological ; Protein Multimerization
Chemical Substances	Amyloid beta-Peptides ; Azo Compounds ; Buffers ; Peptides ; Protein Aggregates ; azobenzene (F0U1H6UG5C)
Language	English
Publishing date	2018-05-09
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-4939-7811-3_25
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Article ; Online: Proteome-Wide Profiling of Cellular Targets Modified by Dopamine Metabolites Using a Bio-Orthogonally Functionalized Catecholamine.

Hurben, Alexander K / Erber, Luke N / Tretyakova, Natalia Y / Doran, Todd M

ACS chemical biology

2021 Volume 16, Issue 11, Page(s) 2581–2594

Abstract: Selective death of midbrain dopaminergic neurons is a hallmark pathology of Parkinson's disease (PD), but the molecular mechanisms that initiate the cascade of events resulting in neurodegeneration in PD remain unclear. Compelling evidence suggests that ... ...

Abstract	Selective death of midbrain dopaminergic neurons is a hallmark pathology of Parkinson's disease (PD), but the molecular mechanisms that initiate the cascade of events resulting in neurodegeneration in PD remain unclear. Compelling evidence suggests that dysregulation of dopamine (DA) induces neuronal stress and damage responses that are operative processes in striatal degeneration preceding PD-like symptoms. Improper DA sequestration to vesicles raises cytosolic DA levels, which is rapidly converted into electrophilic dopaquinone species (DQs) that react readily with protein nucleophiles forming covalent modifications that alter the native structure and function of proteins. These so-called DA-protein adducts (DPAs) have been reported to play a role in neurotoxicity, and their abundance with respect to neurodegeneration has been linked to clinical and pathological features of PD that suggest that they play a causal role in PD pathogenesis. Therefore, characterizing DPAs is a critical first step in understanding the susceptibility of midbrain dopaminergic neurons during PD. To help achieve this goal, we report here a novel DA-mimetic (DA
MeSH term(s)	Catecholamines/metabolism ; Dopamine/metabolism ; Dopamine/toxicity ; Dopaminergic Neurons/metabolism ; Endoplasmic Reticulum Stress ; Humans ; Oxidation-Reduction ; Parkinson Disease/metabolism ; Parkinson Disease/pathology ; Protein Disulfide-Isomerases/metabolism ; Proteome ; Proteomics/methods
Chemical Substances	Catecholamines ; Proteome ; Protein Disulfide-Isomerases (EC 5.3.4.1) ; Dopamine (VTD58H1Z2X)
Language	English
Publishing date	2021-11-02
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ISSN	1554-8937
ISSN (online)	1554-8937
DOI	10.1021/acschembio.1c00629
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Article ; Online: Chemoselective Bioconjugation of Amyloidogenic Protein Antigens to PEGylated Microspheres Enables Detection of α-Synuclein Autoantibodies in Human Plasma.

Ge, Peng / Yang, Mu / Bouchard, Jacob L / Dzamko, Nicolas / Lewis, Simon J G / Halliday, Glenda M / Doran, Todd M

Bioconjugate chemistry

2022 Volume 33, Issue 2, Page(s) 301–310

Abstract: The misfolding and subsequent aggregation of amyloidogenic proteins is a classic pathological hallmark of neurodegenerative diseases. Aggregates of the α-synuclein protein (αS) are implicated in Parkinson's disease (PD) pathogenesis, and naturally ... ...

Abstract	The misfolding and subsequent aggregation of amyloidogenic proteins is a classic pathological hallmark of neurodegenerative diseases. Aggregates of the α-synuclein protein (αS) are implicated in Parkinson's disease (PD) pathogenesis, and naturally occurring autoantibodies to these aggregates are proposed to be potential early-stage biomarkers to facilitate the diagnosis of PD. However, upon misfolding, αS forms a multitude of quaternary structures of varying functions that are unstable
MeSH term(s)	Amyloidogenic Proteins ; Autoantibodies ; Humans ; Microspheres ; Parkinson Disease/diagnosis ; Polyethylene Glycols ; alpha-Synuclein/chemistry
Chemical Substances	Amyloidogenic Proteins ; Autoantibodies ; alpha-Synuclein ; Polyethylene Glycols (3WJQ0SDW1A)
Language	English
Publishing date	2022-01-12
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1024041-x
ISSN	1520-4812 ; 1043-1802
ISSN (online)	1520-4812
ISSN	1043-1802
DOI	10.1021/acs.bioconjchem.1c00530
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Article: Photocaged dicarbonyl probe provides spatiotemporal control over protein glycation

Hurben, Alexander K. / Ge, Peng / Bouchard, Jacob L. / Doran, Todd M. / Tretyakova, Natalia Y.

Chemical communications. 2022 Jan. 18, v. 58, no. 6

2022

Abstract	Protein glycation is a disease associated, non-enzymatic, posttranslational modification generated by endogenous dicarbonyl metabolites. Currently, there is a lack of chemical tools capable of studying protein adducts caused by this class of reactive species. Here, we report a chemical biology platform, termed T-DiP (targetable-dicarbonyl precursor), that releases a physiologically relevant dose of bio-orthogonally functionalized dicarbonyl probe upon irradiation with 365 nm light. This approach enables protein glycation to be controlled with spatiotemporal precision within live cells and expands the chemical toolbox needed to elucidate the roles of glycated proteins across various pathologies.
Keywords	glycation ; irradiation ; metabolites ; post-translational modification
Language	English
Dates of publication	2022-0118
Size	p. 855-858.
Publishing place	The Royal Society of Chemistry
Document type	Article
ZDB-ID	1472881-3
ISSN	1364-548X ; 1359-7345 ; 0009-241X
ISSN (online)	1364-548X
ISSN	1359-7345 ; 0009-241X
DOI	10.1039/d1cc06651j
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Aβ(M1-40) and Wild-Type Aβ40 Self-Assemble into Oligomers with Distinct Quaternary Structures.

Bouchard, Jacob L / Davey, Taylor C / Doran, Todd M

Molecules (Basel, Switzerland)

2019 Volume 24, Issue 12

Abstract: Amyloid-β oligomers (AβOs) self-assemble into polymorphic species with diverse biological activities that are implicated causally to Alzheimer's disease (AD). Synaptotoxicity of AβO species is dependent on their quaternary structure, however, low- ... ...

Abstract	Amyloid-β oligomers (AβOs) self-assemble into polymorphic species with diverse biological activities that are implicated causally to Alzheimer's disease (AD). Synaptotoxicity of AβO species is dependent on their quaternary structure, however, low-abundance and environmental sensitivity of AβOs in vivo have impeded a thorough assessment of structure-function relationships. We developed a simple biochemical assay to quantify the relative abundance and morphology of cross-linked AβOs. We compared oligomers derived from synthetic Aβ40 (wild-type (WT) Aβ40) and a recombinant source, called Aβ(M1-40). Both peptides assemble into oligomers with common sizes and morphology, however, the predominant quaternary structures of Aβ(M1-40) oligomeric states were more diverse in terms of dispersity and morphology. We identified self-assembly conditions that stabilize high-molecular weight oligomers of Aβ(M1-40) with apparent molecular weights greater than 36 kDa. Given that mixtures of AβOs derived from both peptides have been shown to be potent neurotoxins that disrupt long-term potentiation, we anticipate that the diverse quaternary structures reported for Aβ(M1-40) oligomers using the assays reported here will facilitate research efforts aimed at isolating and identifying common toxic species that contribute to synaptic dysfunction.
MeSH term(s)	Amyloid beta-Peptides/chemistry ; Amyloid beta-Peptides/genetics ; Humans ; Mutation ; Native Polyacrylamide Gel Electrophoresis ; Protein Aggregates ; Protein Aggregation, Pathological ; Protein Folding ; Protein Multimerization ; Protein Structure, Quaternary ; Recombinant Proteins ; Structure-Activity Relationship
Chemical Substances	Amyloid beta-Peptides ; Protein Aggregates ; Recombinant Proteins
Language	English
Publishing date	2019-06-15
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1413402-0
ISSN	1420-3049 ; 1431-5165 ; 1420-3049
ISSN (online)	1420-3049
ISSN	1431-5165 ; 1420-3049
DOI	10.3390/molecules24122242
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Article ; Online: Pulmonary Arterial Hypertension and Intraductal Papillary Mucinous Neoplasms of the Pancreas: A Novel Association?

Lee, Michael H / Doran, Jennifer / Bang, Tami J / Hohsfield, Robin / Hountras, Peter / Boddie, Genevieve / Wagh, Mihir S / Badesch, David / Bull, Todd M

Chest

2021 Volume 160, Issue 6, Page(s) 2260–2265

MeSH term(s)	Adenocarcinoma, Mucinous/complications ; Adenocarcinoma, Mucinous/diagnostic imaging ; Adenocarcinoma, Mucinous/therapy ; Cholangiopancreatography, Magnetic Resonance ; Female ; Humans ; Male ; Pancreatic Intraductal Neoplasms/complications ; Pancreatic Intraductal Neoplasms/diagnostic imaging ; Pancreatic Intraductal Neoplasms/therapy ; Pancreatic Neoplasms/complications ; Pancreatic Neoplasms/diagnostic imaging ; Pancreatic Neoplasms/therapy ; Pulmonary Arterial Hypertension/complications ; Pulmonary Arterial Hypertension/therapy ; Vascular Resistance
Language	English
Publishing date	2021-07-17
Publishing country	United States
Document type	Case Reports ; Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	1032552-9
ISSN	1931-3543 ; 0012-3692
ISSN (online)	1931-3543
ISSN	0012-3692
DOI	10.1016/j.chest.2021.06.078
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Article ; Online: Aβ(M1–40) and Wild-Type Aβ40 Self-Assemble into Oligomers with Distinct Quaternary Structures

Jacob L. Bouchard / Taylor C. Davey / Todd M. Doran

Molecules, Vol 24, Iss 12, p

2019 Volume 2242

Abstract: Amyloid-β oligomers (AβOs) self-assemble into polymorphic species with diverse biological activities that are implicated causally to Alzheimer’s disease (AD). Synaptotoxicity of AβO species is dependent on their quaternary structure, however, low- ... ...

Abstract	Amyloid-β oligomers (AβOs) self-assemble into polymorphic species with diverse biological activities that are implicated causally to Alzheimer’s disease (AD). Synaptotoxicity of AβO species is dependent on their quaternary structure, however, low-abundance and environmental sensitivity of AβOs in vivo have impeded a thorough assessment of structure−function relationships. We developed a simple biochemical assay to quantify the relative abundance and morphology of cross-linked AβOs. We compared oligomers derived from synthetic Aβ40 (wild-type (WT) Aβ40) and a recombinant source, called Aβ(M1−40). Both peptides assemble into oligomers with common sizes and morphology, however, the predominant quaternary structures of Aβ(M1−40) oligomeric states were more diverse in terms of dispersity and morphology. We identified self-assembly conditions that stabilize high-molecular weight oligomers of Aβ(M1−40) with apparent molecular weights greater than 36 kDa. Given that mixtures of AβOs derived from both peptides have been shown to be potent neurotoxins that disrupt long-term potentiation, we anticipate that the diverse quaternary structures reported for Aβ(M1−40) oligomers using the assays reported here will facilitate research efforts aimed at isolating and identifying common toxic species that contribute to synaptic dysfunction.
Keywords	Alzheimer’s disease ; Amyloid-β ; recombinant Aβ ; oligomers ; low-molecular weight (LMW) oligomers ; high-molecular weight (HMW) oligomers ; quaternary structure ; morphology ; conformation ; PICUP ; Organic chemistry ; QD241-441
Language	English
Publishing date	2019-06-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Chemical Tools To Monitor and Manipulate Adaptive Immune Responses.

Doran, Todd M / Sarkar, Mohosin / Kodadek, Thomas

Journal of the American Chemical Society

2016 Volume 138, Issue 19, Page(s) 6076–6094

Abstract: Methods to monitor and manipulate the immune system are of enormous clinical interest. For example, the development of vaccines represents one of the earliest and greatest accomplishments of the biomedical research enterprise. More recently, drugs ... ...

Abstract	Methods to monitor and manipulate the immune system are of enormous clinical interest. For example, the development of vaccines represents one of the earliest and greatest accomplishments of the biomedical research enterprise. More recently, drugs capable of "reawakening" the immune system to cancer have generated enormous excitement. But, much remains to be done. All drugs available today that manipulate the immune system cannot distinguish between "good" and "bad" immune responses and thus drive general and systemic immune suppression or activation. Indeed, with the notable exception of vaccines, our ability to monitor and manipulate antigen-specific immune responses is in its infancy. Achieving this finer level of control would be highly desirable. For example, it might allow the pharmacological editing of pathogenic immune responses without restricting the ability of the immune system to defend against infection. On the diagnostic side, a method to comprehensively monitor the circulating, antigen-specific antibody population could provide a treasure trove of clinically useful biomarkers, since many diseases expose the immune system to characteristic molecules that are deemed foreign and elicit the production of antibodies against them. This Perspective will discuss the state-of-the-art of this area with a focus on what we consider seminal opportunities for the chemistry community to contribute to this important field.
MeSH term(s)	Adaptive Immunity/drug effects ; Adjuvants, Immunologic/pharmacology ; Animals ; Antibodies/chemistry ; Antibodies/pharmacology ; Epitopes/chemistry ; Humans ; Immunosuppressive Agents/pharmacology ; Monitoring, Physiologic
Chemical Substances	Adjuvants, Immunologic ; Antibodies ; Epitopes ; Immunosuppressive Agents
Language	English
Publishing date	2016-05-03
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. ; Review
ZDB-ID	3155-0
ISSN	1520-5126 ; 0002-7863
ISSN (online)	1520-5126
ISSN	0002-7863
DOI	10.1021/jacs.6b02954
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