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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

Shelf mark	Loan status	Location
Zs A 7042 -1777-	verfügbar in Königswinter	Königswinter

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Article ; Online: Peptide Self-Assembly into Amyloid Fibrils: Unbiased All-Atom Simulations.

Nilsson, Bradley L / Celebi Torabfam, Gizem / Dias, Cristiano L

The journal of physical chemistry. B

2024 Volume 128, Issue 14, Page(s) 3320–3328

Abstract: Protein self-assembly plays an important role in biological systems, accounting for the formation of mesoscopic structures that can be highly symmetric as in the capsid of viruses or disordered as in molecular condensates or exhibit a one-dimensional ... ...

Abstract	Protein self-assembly plays an important role in biological systems, accounting for the formation of mesoscopic structures that can be highly symmetric as in the capsid of viruses or disordered as in molecular condensates or exhibit a one-dimensional fibrillar morphology as in amyloid fibrils. Deposits of the latter in tissues of individuals with degenerative diseases like Alzheimer's and Parkinson's has motivated extensive efforts to understand the sequence of molecular events accounting for their formation. These studies aim to identify on-pathway intermediates that may be the targets for therapeutic intervention. This detailed knowledge of fibril formation remains obscure, in part due to challenges with experimental analyses of these processes. However, important progress is being achieved for short amyloid peptides due to advances in our ability to perform completely unbiased all-atom simulations of the self-assembly process. This perspective discusses recent developments, their implications, and the hurdles that still need to be overcome to further advance the field.
MeSH term(s)	Humans ; Amyloid/chemistry ; Amyloid beta-Peptides/chemistry
Chemical Substances	Amyloid ; Amyloid beta-Peptides
Language	English
Publishing date	2024-03-06
Publishing country	United States
Document type	Journal Article ; Review
ISSN	1520-5207
ISSN (online)	1520-5207
DOI	10.1021/acs.jpcb.3c07861
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Solvent Suppression in Pure Shift NMR.

Gates, Emma L / Bradley, Jonathan P / Berry, Daniel B G / Nilsson, Mathias / Morris, Gareth A / Adams, Ralph W / Castañar, Laura

Analytical chemistry

2024 Volume 96, Issue 9, Page(s) 3879–3885

Abstract: Intense solvent signals ... ...

Abstract	Intense solvent signals in
Language	English
Publishing date	2024-02-21
Publishing country	United States
Document type	Journal Article
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.3c05379
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Article ; Online: Supramolecular Phenylalanine-Derived Hydrogels for the Sustained Release of Functional Proteins.

Jagrosse, Melissa L / Agredo, Pamela / Abraham, Brittany L / Toriki, Ethan S / Nilsson, Bradley L

ACS biomaterials science & engineering

2023 Volume 9, Issue 2, Page(s) 784–796

Abstract: Protein-based therapeutics have emerged as next-generation pharmaceutical agents for oncology, bone regeneration, autoimmune disorders, viral infections, and other diseases. The clinical application of protein therapeutics has been impeded by ... ...

Abstract	Protein-based therapeutics have emerged as next-generation pharmaceutical agents for oncology, bone regeneration, autoimmune disorders, viral infections, and other diseases. The clinical application of protein therapeutics has been impeded by pharmacokinetic and pharmacodynamic challenges including off-target toxicity, rapid clearance, and drug stability. Strategies for the localized and sustained delivery of protein therapeutics have shown promise in addressing these challenges. Hydrogels are critical materials that enable these delivery strategies. Supramolecular hydrogels composed of self-assembled materials have demonstrated biocompatibility advantages over polymer hydrogels, with peptide and protein-based gels showing strong potential. However, cost is a significant drawback of peptide-based supramolecular hydrogels. Supramolecular hydrogels composed of inexpensive low-molecular-weight (LMW) gelators, including modified amino acid derivatives, have been reported as viable alternatives to peptide-based materials. Herein, we report the encapsulation and release of proteins from supramolecular hydrogels composed of perfluorinated fluorenylmethyloxcarbonyl-modified phenylalanine (Fmoc-F
MeSH term(s)	Humans ; Hydrogels/chemistry ; Phenylalanine/chemistry ; Delayed-Action Preparations/pharmacology ; Proteins/therapeutic use ; Peptides/chemistry
Chemical Substances	Hydrogels ; Phenylalanine (47E5O17Y3R) ; Delayed-Action Preparations ; Proteins ; Peptides
Language	English
Publishing date	2023-01-24
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, P.H.S.
ISSN	2373-9878
ISSN (online)	2373-9878
DOI	10.1021/acsbiomaterials.2c01299
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Effects of Ions and Small Compounds on the Structure of Aβ

Mahmoudinobar, Farbod / Nilsson, Bradley L / Dias, Cristiano L

The journal of physical chemistry. B

2021 Volume 125, Issue 4, Page(s) 1085–1097

Abstract: Aggregation of amyloid-β (Aβ) proteins in the brain is a hallmark of Alzheimer's disease. This phenomenon can be promoted or inhibited by adding small molecules to the solution where Aβ is embedded. These molecules affect the ensemble of conformations ... ...

Abstract	Aggregation of amyloid-β (Aβ) proteins in the brain is a hallmark of Alzheimer's disease. This phenomenon can be promoted or inhibited by adding small molecules to the solution where Aβ is embedded. These molecules affect the ensemble of conformations sampled by Aβ monomers even before aggregation starts. Here, we perform extensive all-atom replica exchange molecular dynamics (REMD) simulations to provide a comparative study of the ensemble of conformations sampled by Aβ
MeSH term(s)	Alzheimer Disease ; Amyloid beta-Peptides ; Humans ; Hydrophobic and Hydrophilic Interactions ; Molecular Dynamics Simulation ; Peptide Fragments ; Protein Structure, Secondary
Chemical Substances	Amyloid beta-Peptides ; Peptide Fragments
Language	English
Publishing date	2021-01-22
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ISSN	1520-5207
ISSN (online)	1520-5207
DOI	10.1021/acs.jpcb.0c09617
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Article ; Online: Side-chain halogen effects on self-assembly and hydrogelation of cationic phenylalanine derivatives.

Abraham, Brittany L / Mensah, Samantha G / Gwinnell, Benjamin R / Nilsson, Bradley L

Soft matter

2022 Volume 18, Issue 32, Page(s) 5999–6008

Abstract: Low molecular weight (LMW) supramolecular hydrogels have great potential as next-generation biomaterials for drug delivery, tissue engineering, and regenerative medicine. The design of LMW gelators is complicated by the lack of understanding regarding ... ...

Abstract	Low molecular weight (LMW) supramolecular hydrogels have great potential as next-generation biomaterials for drug delivery, tissue engineering, and regenerative medicine. The design of LMW gelators is complicated by the lack of understanding regarding how the chemical structure of the gelator correlates to self-assembly potential and emergent hydrogel material properties. The fluorenylmethyloxycarbonyl-phenylalanine (Fmoc-Phe) motif is a privileged scaffold that is prone to undergo self-assembly into self-supporting hydrogel networks. Cationic Fmoc-Phe-DAP derivatives modified with diaminopropane (DAP) at the C-terminus have been developed that self-assemble into hydrogel networks in aqueous solutions of sufficient ionic strength. We report herein the impact of side-chain halogenation on the self-assembly and hydrogelation properties of Fmoc-Phe-DAP derivatives. A systematic study of the self-assembly and hydrogelation of monohalogenated Fmoc-Phe-DAP derivatives with F, Cl, or Br atoms in the
MeSH term(s)	Cations ; Halogens ; Hydrogels/chemistry ; Molecular Weight ; Phenylalanine/analogs & derivatives ; Phenylalanine/chemistry
Chemical Substances	Cations ; Fmoc-phenylalanine ; Halogens ; Hydrogels ; Phenylalanine (47E5O17Y3R)
Language	English
Publishing date	2022-08-17
Publishing country	England
Document type	Journal Article
ZDB-ID	2191476-X
ISSN	1744-6848 ; 1744-683X
ISSN (online)	1744-6848
ISSN	1744-683X
DOI	10.1039/d2sm00713d
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Article ; Online: Defining the Landscape of the Pauling-Corey Rippled Sheet: An Orphaned Motif Finding New Homes.

Raskatov, Jevgenij A / Schneider, Joel P / Nilsson, Bradley L

Accounts of chemical research

2021 Volume 54, Issue 10, Page(s) 2488–2501

Abstract: ... composed of mixtures of l- and d-amphiphilic peptides confirmed that the resulting fibrils were composed ... of alternating l/d peptides consistent with rippled β-sheets. It was also demonstrated that mirror-image amyloid ...

Abstract	When peptides are mixed with their mirror images in an equimolar ratio, two-dimensional periodic structural folds can form, in which extended peptide strands are arrayed with alternating chirality. The resultant topography class, termed the rippled β-sheet, was introduced as a theoretical concept by Pauling and Corey in 1953. Unlike other fundamental protein structural motifs identified around that time, including the α-helix and the pleated β-sheet, it took several decades before conclusive experimental data supporting the proposed rippled β-sheet motif were gained. Much of the key experimental evidence was provided over the course of the past decade through the concurrent efforts of our three laboratories. Studies that focused on developing new self-assembling hydrogel materials have shown that certain amphiphilic peptides form fibrils and hydrogel networks that are more rigid and have a higher thermodynamic stability when made from racemic peptide mixtures as opposed to pure enantiomers. Related interrogation of assemblies composed of mixtures of l- and d-amphiphilic peptides confirmed that the resulting fibrils were composed of alternating l/d peptides consistent with rippled β-sheets. It was also demonstrated that mirror-image amyloid beta (Aβ) could act as a molecular chaperone to promote oligomer-to-fibril conversion of the natural Aβ enantiomer, which was found to reduce Aβ neurotoxicity against different neuronal cell models. With a cross-disciplinary approach that combines experiment and theory, our three laboratories have demonstrated the unique biophysical, biochemical, and biological properties that arise upon mixing of peptide enantiomers, in consequence of rippled β-sheet formation. In this Account, we give an overview of the early history of the rippled β-sheet and provide a detailed structural description/definition of this motif relative to the pleated β-sheet. We then summarize the key findings, obtained on three unique sets of aggregating mirror-image peptide pairs through independent efforts of our three laboratories, and use these results to delineate the landscape of the rippled β-sheet structural motif to inspire future studies. Peptide sequence parameters that favor rippled β-sheet assembly are described, along with the accompanying kinetic and thermodynamic properties, as well as the resulting emergent physical properties of the assemblies. The Account then concludes with a brief overview of some key unresolved challenges in this nascent field. There is much potential for future applications of this unique supramolecular motif in the realm of materials design and biomedical research. We hope this Account will stimulate much-needed discussion of this fascinating structural class to eventually produce a fully quantitative, rational framework for the molecular engineering of rippled β-sheets in the future.
MeSH term(s)	Kinetics ; Models, Molecular ; Peptides/chemistry ; Protein Structure, Secondary ; Thermodynamics
Chemical Substances	Peptides
Language	English
Publishing date	2021-04-26
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, N.I.H., Intramural ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
ZDB-ID	1483291-4
ISSN	1520-4898 ; 0001-4842
ISSN (online)	1520-4898
ISSN	0001-4842
DOI	10.1021/acs.accounts.1c00084
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Ultra-selective, ultra-clean 1D rotating-frame Overhauser effect spectroscopy.

Gates, Emma L / Smith, Marshall J / Bradley, Jonathan P / Johnson, Myron / Widmalm, Göran / Nilsson, Mathias / Morris, Gareth A / Adams, Ralph W / Castañar, Laura

Chemical communications (Cambridge, England)

2023 Volume 59, Issue 39, Page(s) 5854–5857

Abstract: An ultra-selective 1D NMR experiment - GEMSTONE-ROESY - enables clear, unambiguous assignment of ROE signals in the not uncommon situation that traditional selective methods fail. Its usefulness is demonstrated in the analysis of the natural products ... ...

Abstract	An ultra-selective 1D NMR experiment - GEMSTONE-ROESY - enables clear, unambiguous assignment of ROE signals in the not uncommon situation that traditional selective methods fail. Its usefulness is demonstrated in the analysis of the natural products cyclosporin and lacto-
Language	English
Publishing date	2023-05-11
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/d3cc00550j
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Article: Hybrid Amyloid Quantum Dot Nanoassemblies to Probe Neuroinflammatory Damage.

Chiang, Wesley / Urban, Jennifer M / Yanchik-Slade, Francine / Stout, Angela / Nilsson, Bradley L / Gelbard, Harris A / Krauss, Todd D

bioRxiv : the preprint server for biology

2023

Abstract: Various oligomeric species of amyloid-beta have been proposed to play different immunogenic roles in the cellular pathology of Alzheimer's Disease. However, investigating the role of a homogenous single oligomeric species has been difficult due to highly ...

Abstract	Various oligomeric species of amyloid-beta have been proposed to play different immunogenic roles in the cellular pathology of Alzheimer's Disease. However, investigating the role of a homogenous single oligomeric species has been difficult due to highly dynamic oligomerization and fibril formation kinetics that convert between many species. Here we report the design and construction of a quantum dot mimetic for larger spherical oligomeric amyloid species as an "endogenously" fluorescent proxy for this cytotoxic species to investigate its role in inducing inflammatory and stress response states in neuronal and glial cell types.
Language	English
Publishing date	2023-09-01
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.08.30.555592
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Article ; Online: Binding Mechanisms of Amyloid-like Peptides to Lipid Bilayers and Effects of Divalent Cations.

Yang, Yanxing / Jalali, Sharareh / Nilsson, Bradley L / Dias, Cristiano L

ACS chemical neuroscience

2021 Volume 12, Issue 11, Page(s) 2027–2035

Abstract: In several neurodegenerative diseases, cell toxicity can emerge from damage produced by amyloid aggregates to lipid membranes. The details accounting for this damage are poorly understood including how individual amyloid peptides interact with ... ...

Abstract	In several neurodegenerative diseases, cell toxicity can emerge from damage produced by amyloid aggregates to lipid membranes. The details accounting for this damage are poorly understood including how individual amyloid peptides interact with phospholipid membranes before aggregation. Here, we use all-atom molecular dynamics simulations to investigate the molecular mechanisms accounting for amyloid-membrane interactions and the role played by calcium ions in this interaction. Model peptides known to self-assemble into amyloid fibrils and bilayer made from zwitterionic and anionic lipids are used in this study. We find that both electrostatic and hydrophobic interactions contribute to peptide-bilayer binding. In particular, the attraction of peptides to lipid bilayers is dominated by electrostatic interactions between positive residues and negative phosphate moieties of lipid head groups. This attraction is stronger for anionic bilayers than for zwitterionic ones. Hydrophobicity drives the burial of nonpolar residues into the interior of the bilayer producing strong binding in our simulations. Moreover, we observe that the attraction of peptides to the bilayer is significantly reduced in the presence of calcium ions. This is due to the binding of calcium ions to negative phosphate moieties of lipid head groups, which leaves phospholipid bilayers with a net positive charge. Strong binding of the peptide to the membrane occurs less frequently in the presence of calcium ions and involves the formation of a "Ca
MeSH term(s)	Amyloid ; Amyloid beta-Peptides ; Cations, Divalent ; Lipid Bilayers ; Molecular Dynamics Simulation
Chemical Substances	Amyloid ; Amyloid beta-Peptides ; Cations, Divalent ; Lipid Bilayers
Language	English
Publishing date	2021-05-11
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ISSN	1948-7193
ISSN (online)	1948-7193
DOI	10.1021/acschemneuro.1c00140
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