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Article ; Online: NMR Relaxation Experiments Probe Monomer-Fibril Interaction and Identify Critical Interacting Residues Responsible for Distinct Tau Fibril Morphologies.

Oliyantakath Hassan, Muhammed Shafeek / Abdul Vahid, Arshad / Sahayaraj, Allwin Ebenezer / Viswanathan, Renjith / Vijayan, Vinesh

The journal of physical chemistry letters

2023 Volume 14, Issue 29, Page(s) 6583–6591

Abstract: Tau aggregation is governed by secondary processes, a major pathological pathway for tau protein fibril propagation, yet its molecular mechanism remains unknown. This work uses saturation transfer and lifetime line-broadening experiments to identify the ... ...

Abstract	Tau aggregation is governed by secondary processes, a major pathological pathway for tau protein fibril propagation, yet its molecular mechanism remains unknown. This work uses saturation transfer and lifetime line-broadening experiments to identify the critical residues involved in these secondary processes. Distinct residue-specific NMR relaxation parameters were obtained for the truncated three repeat tau construct (K19) in equilibrium with structurally different, self-aggregated (saK19) or heparin-induced (hK19) fibrils. The interacting residues are restricted to R3 repeat for hK19 and to R3, R4, and R' repeats for saK19 fibrils. Furthermore, the relaxation profiles of tau monomers in equilibrium with the structurally comparable, in vitro pathological fibrils (tauAD and tauCTE) were similar but distinct from hK19 or saK19 fibrils. Thus, residue-specific relaxation identifies the important residues involved in the binding of monomers to the fibrils. The relaxation profile of the monomers in equilibrium with the NMR invisible fibril seeds potentially distinguishes the distinct structures of tau fibrils.
MeSH term(s)	tau Proteins/chemistry ; Amino Acid Sequence ; Magnetic Resonance Spectroscopy ; Magnetic Resonance Imaging ; Amyloid/chemistry
Chemical Substances	tau Proteins ; Amyloid
Language	English
Publishing date	2023-07-17
Publishing country	United States
Document type	Journal Article
ISSN	1948-7185
ISSN (online)	1948-7185
DOI	10.1021/acs.jpclett.3c00912
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Modulation of Primary and Secondary Processes in Tau Fibril Formation by Salt-Induced Dynamics.

Abdul Vahid, Arshad / Oliyantakath Hassan, Muhammed Shafeek / Sahayaraj, Allwin Ebenezer / Babu, Ann Teres / Kizhakkeduth, Safwa T / Vijayan, Vinesh

ACS chemical neuroscience

2024 Volume 15, Issue 6, Page(s) 1242–1253

Abstract: The initial stages of amyloid fibrilization begin with the monomers populating aggregation-prone conformers. Characterization of such aggregation-prone conformers is crucial in the study of neurodegenerative diseases. The current study characterizes the ... ...

Abstract	The initial stages of amyloid fibrilization begin with the monomers populating aggregation-prone conformers. Characterization of such aggregation-prone conformers is crucial in the study of neurodegenerative diseases. The current study characterizes the aggregation pathway of two tau protein constructs that have been recently demonstrated to form Alzheimer's (AD) fibril structures with divalent ions and chronic traumatic encephalopathy (CTE) fibril structures with monovalent ions. The results highlight the involvement of identical residues in both the primary and secondary processes of both AD and CTE fibril propagation. Nuclear magnetic resonance relaxation experiments reveal increased flexibility of the motifs
MeSH term(s)	Humans ; tau Proteins/metabolism ; Sodium Chloride ; Amyloid/metabolism ; Ions ; Alzheimer Disease/metabolism
Chemical Substances	tau Proteins ; Sodium Chloride (451W47IQ8X) ; Amyloid ; Ions
Language	English
Publishing date	2024-03-03
Publishing country	United States
Document type	Journal Article
ISSN	1948-7193
ISSN (online)	1948-7193
DOI	10.1021/acschemneuro.3c00852
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Article: Ligand-Induced Ground- and Excited-State Chirality in Silicon Nanoparticles: Surface Interactions Matter

Sujith, Meleppatt / Vishnu, E. Krishnan / Sappati, Subrahmanyam / Oliyantakath Hassan, Muhammed Shafeek / Vijayan, Vinesh / Thomas, K. George

Journal of the American Chemical Society. 2022 Mar. 08, v. 144, no. 11

2022

Abstract: Silicon-based light-emitting materials have emerged as a favorable substitute to various organic and inorganic systems due to silicon’s high natural abundance, low toxicity, and excellent biocompatibility. However, efforts on the design of free-standing ... ...

Abstract	Silicon-based light-emitting materials have emerged as a favorable substitute to various organic and inorganic systems due to silicon’s high natural abundance, low toxicity, and excellent biocompatibility. However, efforts on the design of free-standing silicon nanoparticles with chiral non-racemic absorption and emission attributes are rather scare. Herein, we unravel the structural requirements for ligand-induced chirality in silicon-based nanomaterials by functionalizing with D- and L-isomers of a bifunctional ligand, namely, tryptophan. The structural aspects of these systems are established using high-resolution high-angle annular dark-field imaging in the scanning transmission electron microscopy mode, solid-state nuclear magnetic resonance, Fourier transform infrared, and X-ray photoelectron spectroscopy. Silicon nanoparticles capped with L- and D-isomers of tryptophan displayed positive and negative monosignated circular dichroic signals and circularly polarized luminescence indicating their ground- and excited-state chirality. Various studies supported by density functional theory calculations signify that the functionalization of indole ring nitrogen on the silicon surface plays a decisive role in modifying the chiroptical characteristics by generating emissive charge-transfer states. The chiroptical responses originate from the multipoint interactions of tryptophan with the nanoparticle surface through the indole nitrogen and −CO₂– groups that can transmit an enantiomeric structural imprint on the silicon surface. However, chiroptical properties are not observed in phenylalanine- and alanine-capped silicon nanoparticles, which are devoid of Si–N bonds and chiral footprints. Thus, the ground- and excited-state chiroptics in tryptophan-capped silicon nanoparticles originates from the collective effect of ligand-bound emissive charge-transfer states and chiral footprints. Being the first report on the circularly polarized luminescence in silicon nanoparticles, this work will open newer possibilities in the field of chirality.
Keywords	Fourier transform infrared spectroscopy ; X-ray photoelectron spectroscopy ; absorption ; biocompatibility ; density functional theory ; indoles ; ligands ; luminescence ; nitrogen ; nuclear magnetic resonance spectroscopy ; optical isomerism ; silicon ; toxicity ; transmission electron microscopy ; tryptophan
Language	English
Dates of publication	2022-0308
Size	p. 5074-5086.
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/jacs.1c13698
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Article ; Online: Ligand-Induced Ground- and Excited-State Chirality in Silicon Nanoparticles: Surface Interactions Matter.

Sujith, Meleppatt / Vishnu, E Krishnan / Sappati, Subrahmanyam / Oliyantakath Hassan, Muhammed Shafeek / Vijayan, Vinesh / Thomas, K George

Journal of the American Chemical Society

2022 Volume 144, Issue 11, Page(s) 5074–5086

Abstract: Silicon-based light-emitting materials have emerged as a favorable substitute to various organic and inorganic systems due to silicon's high natural abundance, low toxicity, and excellent biocompatibility. However, efforts on the design of free-standing ... ...

Abstract	Silicon-based light-emitting materials have emerged as a favorable substitute to various organic and inorganic systems due to silicon's high natural abundance, low toxicity, and excellent biocompatibility. However, efforts on the design of free-standing silicon nanoparticles with chiral non-racemic absorption and emission attributes are rather scare. Herein, we unravel the structural requirements for ligand-induced chirality in silicon-based nanomaterials by functionalizing with D- and L-isomers of a bifunctional ligand, namely, tryptophan. The structural aspects of these systems are established using high-resolution high-angle annular dark-field imaging in the scanning transmission electron microscopy mode, solid-state nuclear magnetic resonance, Fourier transform infrared, and X-ray photoelectron spectroscopy. Silicon nanoparticles capped with L- and D-isomers of tryptophan displayed positive and negative monosignated circular dichroic signals and circularly polarized luminescence indicating their ground- and excited-state chirality. Various studies supported by density functional theory calculations signify that the functionalization of indole ring nitrogen on the silicon surface plays a decisive role in modifying the chiroptical characteristics by generating emissive charge-transfer states. The chiroptical responses originate from the multipoint interactions of tryptophan with the nanoparticle surface through the indole nitrogen and -CO
MeSH term(s)	Indoles ; Ligands ; Nanoparticles/chemistry ; Nitrogen ; Silicon/chemistry ; Tryptophan
Chemical Substances	Indoles ; Ligands ; Tryptophan (8DUH1N11BX) ; Nitrogen (N762921K75) ; Silicon (Z4152N8IUI)
Language	English
Publishing date	2022-03-08
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	3155-0
ISSN	1520-5126 ; 0002-7863
ISSN (online)	1520-5126
ISSN	0002-7863
DOI	10.1021/jacs.1c13698
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Article: Mapping the Fibril Core of the Prion Subdomain of the Mammalian CPEB3 that is Involved in Long Term Memory Retention

Reselammal, Dhanya S / Pinhero, Faina / Sharma, Rahul / Oliyantakath Hassan, Muhammed Shafeek / Srinivasula, Srinivasa M / Vijayan, Vinesh

Journal of molecular biology. 2021 July 23, v. 433, no. 15

2021

Abstract: Long-term memory storage is modulated by the prion nature of CPEB3 forming the molecular basis for the maintenance of synaptic facilitation. Here we report that the first prion sub-domain PRD1 of mouse CPEB3 can autonomously form amyloid fibrils in vitro ...

Abstract	Long-term memory storage is modulated by the prion nature of CPEB3 forming the molecular basis for the maintenance of synaptic facilitation. Here we report that the first prion sub-domain PRD1 of mouse CPEB3 can autonomously form amyloid fibrils in vitro and punctate-like structures in vivo. A ninety-four amino acid sequence within the PRD1 domain, PRD1-core, displays high propensity towards aggregation and associated amyloid characteristics. PRD1-core is characterized using electron microscopy, X-ray diffraction, and solution-state NMR deuterium exchange experiments. Secondary structure elements deduced from solid-state NMR reveal a β-rich core comprising of forty amino acids at the N-terminus of PRD1-core. The synthesized twenty-three amino acid long peptide containing the longest rigid segment (E124-H145) of the PRD1-core rapidly self-aggregates and forms fibrils, indicating a limited aggregation-prone region that could potentially activate the aggregation of the full-length protein. This study provides the first step in identifying the structural trigger for the CPEB3 aggregation process.
Keywords	X-ray diffraction ; amino acid sequences ; amino acids ; amyloid ; deuterium ; electron microscopy ; memory ; mice ; molecular biology ; peptides ; prions
Language	English
Dates of publication	2021-0723
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2021.167084
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Article ; Online: Mapping the Fibril Core of the Prion Subdomain of the Mammalian CPEB3 that is Involved in Long Term Memory Retention.

Reselammal, Dhanya S / Pinhero, Faina / Sharma, Rahul / Oliyantakath Hassan, Muhammed Shafeek / Srinivasula, Srinivasa M / Vijayan, Vinesh

Journal of molecular biology

2021 Volume 433, Issue 15, Page(s) 167084

Abstract	Long-term memory storage is modulated by the prion nature of CPEB3 forming the molecular basis for the maintenance of synaptic facilitation. Here we report that the first prion sub-domain PRD1 of mouse CPEB3 can autonomously form amyloid fibrils in vitro and punctate-like structures in vivo. A ninety-four amino acid sequence within the PRD1 domain, PRD1-core, displays high propensity towards aggregation and associated amyloid characteristics. PRD1-core is characterized using electron microscopy, X-ray diffraction, and solution-state NMR deuterium exchange experiments. Secondary structure elements deduced from solid-state NMR reveal a β-rich core comprising of forty amino acids at the N-terminus of PRD1-core. The synthesized twenty-three amino acid long peptide containing the longest rigid segment (E124-H145) of the PRD1-core rapidly self-aggregates and forms fibrils, indicating a limited aggregation-prone region that could potentially activate the aggregation of the full-length protein. This study provides the first step in identifying the structural trigger for the CPEB3 aggregation process.
Language	English
Publishing date	2021-05-31
Publishing country	England
Document type	Journal Article ; 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.2021.167084
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Article ; Online: Examining the Transient Dark State in Protein-Quantum Dot Interaction by Relaxation-Based Solution NMR.

Oliyantakath Hassan, Muhammed Shafeek / Somasundaran, Sanoop Mambully / Abdul Shukkoor, Muhammed Bilal / Ayyappan, Shine / Abdul Vahid, Arshad / Vijayan, Vinesh

The journal of physical chemistry. B

2021 Volume 125, Issue 36, Page(s) 10119–10125

Abstract: We probed the "dark" state involved in the protein-quantum dot (QD) interaction using a relaxation-based solution nuclear magnetic resonance (NMR) approach. We examined the dynamics and exchange kinetics of the ubiquitin-CdTe model system, which ... ...

Abstract	We probed the "dark" state involved in the protein-quantum dot (QD) interaction using a relaxation-based solution nuclear magnetic resonance (NMR) approach. We examined the dynamics and exchange kinetics of the ubiquitin-CdTe model system, which undergoes a fast exchange in the transverse relaxation time scale. We applied the recently developed dark-state exchange saturation transfer (DEST), lifetime line broadening (Δ
MeSH term(s)	Cadmium Compounds ; Magnetic Resonance Spectroscopy ; Nuclear Magnetic Resonance, Biomolecular ; Quantum Dots ; Tellurium
Chemical Substances	Cadmium Compounds ; Tellurium (NQA0O090ZJ) ; cadmium telluride (STG188WO13)
Language	English
Publishing date	2021-09-02
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1520-5207
ISSN (online)	1520-5207
DOI	10.1021/acs.jpcb.1c04853
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Article: Examining the Transient Dark State in Protein-Quantum Dot Interaction by Relaxation-Based Solution NMR

Oliyantakath Hassan, Muhammed Shafeek / Somasundaran, Sanoop Mambully / Abdul Shukkoor, Muhammed Bilal / Ayyappan, Shine / Abdul Vahid, Arshad / Vijayan, Vinesh

Journal of physical chemistry. 2021 Sept. 02, v. 125, no. 36

2021

Abstract: We probed the “dark” state involved in the protein-quantum dot (QD) interaction using a relaxation-based solution nuclear magnetic resonance (NMR) approach. We examined the dynamics and exchange kinetics of the ubiquitin-CdTe model system, which ... ...

Abstract	We probed the “dark” state involved in the protein-quantum dot (QD) interaction using a relaxation-based solution nuclear magnetic resonance (NMR) approach. We examined the dynamics and exchange kinetics of the ubiquitin-CdTe model system, which undergoes a fast exchange in the transverse relaxation time scale. We applied the recently developed dark-state exchange saturation transfer (DEST), lifetime line broadening (ΔR₂), and exchange-induced chemical shift (δₑₓ) solution NMR techniques to obtain a residue-specific binding behavior of the protein on the QD surface. The variation in the estimated ¹⁵N–R₂ᵇᵒᵘⁿᵈ values clearly shows the dynamic nature of bound Ub. Upon mapping the amino acid residues showing a faster relaxation rate on the electrostatic potential surface of the protein, we have determined that the interaction is preferably electrostatic, and the amino acid residues involved in binding lie on the positively charged surface of the protein. We believe that our experimental approach should provide more in-depth knowledge to engineer new hybrid protein-QD systems in the future.
Keywords	amino acids ; hybrids ; nuclear magnetic resonance spectroscopy ; physical chemistry
Language	English
Dates of publication	2021-0902
Size	p. 10119-10125.
Publishing place	American Chemical Society
Document type	Article
ISSN	1520-5207
DOI	10.1021/acs.jpcb.1c04853
Database	NAL-Catalogue (AGRICOLA)

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