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Article ; Online: Editorial for "Rich Club Reorganization in Nurses Before and After the Onset of Occupational Burnout: A Longitudinal MRI Study".

Cheung, Matthew M / Chan, Kevin C

Journal of magnetic resonance imaging : JMRI

2024

Language	English
Publishing date	2024-02-16
Publishing country	United States
Document type	Editorial
ZDB-ID	1146614-5
ISSN	1522-2586 ; 1053-1807
ISSN (online)	1522-2586
ISSN	1053-1807
DOI	10.1002/jmri.29301
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Zs.MO 236: Show issues

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Article ; Online: In silico design of high-affinity antigenic peptides for HLA-B44.

Feng, Mei / Chan, Kevin C / Zhong, Qinglu / Zhou, Ruhong

International journal of biological macromolecules

2024 Volume 267, Issue Pt 2, Page(s) 131356

Abstract: Cancer cell-killing by CD8+ T cells demands effective tumor antigen presentation by human leukocyte antigen class I (HLA-I) molecules. Screening and designing highly immunogenic neoantigens require quantitative computations to reliably predict HLA- ... ...

Abstract	Cancer cell-killing by CD8+ T cells demands effective tumor antigen presentation by human leukocyte antigen class I (HLA-I) molecules. Screening and designing highly immunogenic neoantigens require quantitative computations to reliably predict HLA-peptide binding affinities. Here, with all-atom molecular dynamics (MD) simulations and free energy perturbation (FEP) methods, we design a collection of antigenic peptide candidates through in silico mutagenesis studies on immunogenic neoantigens, yielding enhanced binding affinities to HLA-B44:02. In-depth structural dissection shows that introducing positively charged residues such as arginine to position 6 or lysine to position 7 of the candidates triggers conformational shifts in both peptides and the antigen-binding groove of the HLA, following the "induced-fit" mechanism. Enhancement in binding affinities compared to the wild-type was found in three out of five mutated candidates. The HLA pocket, capable of accommodating positively charged residues in positions from 5 to 7, is designated as the "dynamic pocket". Taken together, we showcase an effective structure-based binding affinity optimization framework for antigenic peptides of HLA-B44:02 and underscore the importance of dynamic nature of the antigen-binding groove in concert with the anchoring motifs. This work provides structural insights for rational design of favorable HLA-peptide bindings and future developments in neoantigen-based therapeutics.
MeSH term(s)	Humans ; Molecular Dynamics Simulation ; Peptides/chemistry ; Peptides/immunology ; Protein Binding ; HLA-B44 Antigen/chemistry ; HLA-B44 Antigen/immunology ; HLA-B44 Antigen/genetics ; Computer Simulation ; Binding Sites ; Protein Conformation
Chemical Substances	Peptides ; HLA-B44 Antigen
Language	English
Publishing date	2024-04-02
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	282732-3
ISSN	1879-0003 ; 0141-8130
ISSN (online)	1879-0003
ISSN	0141-8130
DOI	10.1016/j.ijbiomac.2024.131356
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Zs.B 2374: Show issues

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Article ; Online: Novel Inhibitory Role of Fenofibric Acid by Targeting Cryptic Site on the RBD of SARS-CoV-2.

Huang, Jianxiang / Chan, Kevin C / Zhou, Ruhong

Biomolecules

2023 Volume 13, Issue 2

Abstract: The emergence of the recent pandemic causing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has created an alarming situation worldwide. It also prompted extensive research on drug repurposing to find a potential treatment for SARS-CoV-2 ... ...

Abstract	The emergence of the recent pandemic causing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has created an alarming situation worldwide. It also prompted extensive research on drug repurposing to find a potential treatment for SARS-CoV-2 infection. An active metabolite of the hyperlipidemic drug fenofibrate (also called fenofibric acid or FA) was found to destabilize the receptor-binding domain (RBD) of the viral spike protein and therefore inhibit its binding to human angiotensin-converting enzyme 2 (hACE2) receptor. Despite being considered as a potential drug candidate for SARS-CoV-2, FA's inhibitory mechanism remains to be elucidated. We used molecular dynamics (MD) simulations to investigate the binding of FA to the RBD of the SARS-CoV-2 spike protein and revealed a potential cryptic FA binding site. Free energy calculations were performed for different FA-bound RBD complexes. The results suggest that the interaction of FA with the cryptic binding site of RBD alters the conformation of the binding loop of RBD and effectively reduces its binding affinity towards ACE2. Our study provides new insights for the design of SARS-CoV-2 inhibitors targeting cryptic sites on the RBD of SARS-CoV-2.
MeSH term(s)	Humans ; SARS-CoV-2/metabolism ; COVID-19 ; Fenofibrate ; Protein Binding ; Spike Glycoprotein, Coronavirus/chemistry ; Molecular Dynamics Simulation
Chemical Substances	spike protein, SARS-CoV-2 ; fenofibric acid (BGF9MN2HU1) ; Fenofibrate (U202363UOS) ; Spike Glycoprotein, Coronavirus
Language	English
Publishing date	2023-02-14
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2701262-1
ISSN	2218-273X ; 2218-273X
ISSN (online)	2218-273X
ISSN	2218-273X
DOI	10.3390/biom13020359
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Article ; Online: Molecular Dynamics Refinement of Open State Serotonin 5-HT

Li, Zoe / Chan, Kevin C / Nickels, Jonathan D / Cheng, Xiaolin

Journal of chemical information and modeling

2023 Volume 63, Issue 4, Page(s) 1196–1207

Abstract: Pentameric ligand-gated ion channels play an important role in mediating fast neurotransmissions. As a member of this receptor family, cation-selective 5- ... ...

Abstract	Pentameric ligand-gated ion channels play an important role in mediating fast neurotransmissions. As a member of this receptor family, cation-selective 5-HT
MeSH term(s)	Molecular Dynamics Simulation ; Serotonin/chemistry ; Serotonin/metabolism ; Cryoelectron Microscopy ; Protein Structure, Secondary ; Ion Transport ; Receptors, Serotonin, 5-HT3/chemistry ; Receptors, Serotonin, 5-HT3/metabolism
Chemical Substances	Serotonin (333DO1RDJY) ; Receptors, Serotonin, 5-HT3
Language	English
Publishing date	2023-02-09
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	190019-5
ISSN	1549-960X ; 0095-2338
ISSN (online)	1549-960X
ISSN	0095-2338
DOI	10.1021/acs.jcim.2c01441
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Article ; Online: Auditory Scene Analysis Principles Improve Image Reconstruction Abilities of Novice Vision-to-Audio Sensory Substitution Users.

Hamilton-Fletcher, Giles / Chan, Kevin C

Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference

2021 Volume 2021, Page(s) 5868–5871

Abstract: Sensory substitution devices (SSDs) such as the 'vOICe' preserve visual information in sound by turning visual height, brightness, and laterality into auditory pitch, volume, and panning/time respectively. However, users have difficulty identifying or ... ...

Abstract	Sensory substitution devices (SSDs) such as the 'vOICe' preserve visual information in sound by turning visual height, brightness, and laterality into auditory pitch, volume, and panning/time respectively. However, users have difficulty identifying or tracking multiple simultaneously presented tones - a skill necessary to discriminate the upper and lower edges of object shapes. We explore how these deficits can be addressed by using image-sonifications inspired by auditory scene analysis (ASA). Here, sighted subjects (N=25) of varying musical experience listened to, and then reconstructed, complex shapes consisting of simultaneously presented upper and lower lines. Complex shapes were sonified using the vOICe, with either the upper and lower lines varying only in pitch (i.e. the vOICe's 'unaltered' default settings), or with one line degraded to alter its auditory timbre or volume. Results found that overall performance increased with subjects' years of prior musical experience. ANOVAs revealed that both sonification style and musical experience significantly affected performance, but with no interaction effect between them. Compared to the vOICe's 'unaltered' pitch-height mapping, subjects had significantly better image-reconstruction abilities when the lower line was altered via timbre or volume-modulation. By contrast, altering the upper line only helped users identify the unaltered lower line. In conclusion, adding ASA principles to vision-to-audio SSDs boosts subjects' image-reconstruction abilities, even if this also reduces total task-relevant information. Future SSDs should seek to exploit these findings to enhance both novice user abilities and the use of SSDs as visual rehabilitation tools.
MeSH term(s)	Auditory Perception ; Functional Laterality ; Humans ; Image Processing, Computer-Assisted ; Sound ; Vision, Ocular
Language	English
Publishing date	2021-11-25
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ISSN	2694-0604
ISSN (online)	2694-0604
DOI	10.1109/EMBC46164.2021.9630296
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Article ; Online: GABA decrease is associated with degraded neural specificity in the visual cortex of glaucoma patients.

Bang, Ji Won / Parra, Carlos / Yu, Kevin / Wollstein, Gadi / Schuman, Joel S / Chan, Kevin C

Communications biology

2023 Volume 6, Issue 1, Page(s) 679

Abstract: Glaucoma is an age-related neurodegenerative disease of the visual system, affecting both the eye and the brain. Yet its underlying metabolic mechanisms and neurobehavioral relevance remain largely unclear. Here, using proton magnetic resonance ... ...

Abstract	Glaucoma is an age-related neurodegenerative disease of the visual system, affecting both the eye and the brain. Yet its underlying metabolic mechanisms and neurobehavioral relevance remain largely unclear. Here, using proton magnetic resonance spectroscopy and functional magnetic resonance imaging, we investigated the GABAergic and glutamatergic systems in the visual cortex of glaucoma patients, as well as neural specificity, which is shaped by GABA and glutamate signals and underlies efficient sensory and cognitive functions. Our study shows that among the older adults, both GABA and glutamate levels decrease with increasing glaucoma severity regardless of age. Further, our study shows that the reduction of GABA but not glutamate predicts the neural specificity. This association is independent of the impairments on the retina structure, age, and the gray matter volume of the visual cortex. Our results suggest that glaucoma-specific decline of GABA undermines neural specificity in the visual cortex and that targeting GABA could improve the neural specificity in glaucoma.
MeSH term(s)	Humans ; Aged ; Neurodegenerative Diseases ; Cognition ; Visual Cortex/diagnostic imaging ; Glutamic Acid ; Glaucoma/diagnosis ; gamma-Aminobutyric Acid
Chemical Substances	Glutamic Acid (3KX376GY7L) ; gamma-Aminobutyric Acid (56-12-2)
Language	English
Publishing date	2023-06-29
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ISSN	2399-3642
ISSN (online)	2399-3642
DOI	10.1038/s42003-023-04918-8
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Article ; Online: Accuracy and Usability of Smartphone-Based Distance Estimation Approaches for Visual Assistive Technology Development.

Hamilton-Fletcher, Giles / Liu, Mingxin / Sheng, Diwei / Feng, Chen / Hudson, Todd E / Rizzo, John-Ross / Chan, Kevin C

IEEE open journal of engineering in medicine and biology

2024 Volume 5, Page(s) 54–58

Abstract: Goal: ...

Abstract	Goal:
Language	English
Publishing date	2024-01-25
Publishing country	United States
Document type	Journal Article
ISSN	2644-1276
ISSN (online)	2644-1276
DOI	10.1109/OJEMB.2024.3358562
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Visual Plasticity in Adulthood: Perspectives from Hebbian and Homeostatic Plasticity.

Bang, Ji Won / Hamilton-Fletcher, Giles / Chan, Kevin C

The Neuroscientist : a review journal bringing neurobiology, neurology and psychiatry

2021 Volume 29, Issue 1, Page(s) 117–138

Abstract: The visual system retains profound plastic potential in adulthood. In the current review, we summarize the evidence of preserved plasticity in the adult visual system during visual perceptual learning as well as both monocular and binocular visual ... ...

Abstract	The visual system retains profound plastic potential in adulthood. In the current review, we summarize the evidence of preserved plasticity in the adult visual system during visual perceptual learning as well as both monocular and binocular visual deprivation. In each condition, we discuss how such evidence reflects two major cellular mechanisms of plasticity: Hebbian and homeostatic processes. We focus on how these two mechanisms work together to shape plasticity in the visual system. In addition, we discuss how these two mechanisms could be further revealed in future studies investigating cross-modal plasticity in the visual system.
MeSH term(s)	Adult ; Humans ; Homeostasis ; Neuronal Plasticity ; Visual Cortex
Language	English
Publishing date	2021-08-12
Publishing country	United States
Document type	Review ; Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1233753-5
ISSN	1089-4098 ; 1073-8584
ISSN (online)	1089-4098
ISSN	1073-8584
DOI	10.1177/10738584211037619
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ab Jg. 2022: Lesesaal (EG)

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Article ; Online: Electrostatic Contributions to the Binding Free Energy of Nicotine to the Acetylcholine Binding Protein.

Li, Zoe / Chan, Kevin C / Nickels, Jonathan D / Cheng, Xiaolin

The journal of physical chemistry. B

2022 Volume 126, Issue 43, Page(s) 8669–8679

Abstract: Biomolecular binding relies on specific attractive interactions between two partner molecules, including electrostatics, dispersion, hydrophobicity, and solvation. Assessing the contributions of electrostatic interactions to binding is key to the ... ...

Abstract	Biomolecular binding relies on specific attractive interactions between two partner molecules, including electrostatics, dispersion, hydrophobicity, and solvation. Assessing the contributions of electrostatic interactions to binding is key to the understanding of ligand binding mechanisms and the design of improved biomolecular binders. For example, nicotine is a well-known agonist of nicotinic acetylcholine receptors (nAChRs), but the molecular mechanisms for the differential action of nicotine on brain and muscle nAChRs remain elusive. In this work, we have chosen the acetylcholine binding protein (AChBP) in complex with nicotine as a model system to interrogate the electrostatic contributions to nicotine binding. Our absolute binding free energy simulations confirm that nicotine binds AChBP predominantly in its protonated (charged) form. By comparing energetic contributions from decomposed interactions for either neutral or charged nicotine, our calculations shed light on the nature of the binding of nicotine to the AChBP. The preferred binding of charged nicotine over neutral nicotine originates from its stronger electrostatic interactions with AChBP, a cation-π interaction to a tryptophan residue and a hydrogen bond between nicotine and the backbone carbonyl of the tryptophan, whereas the major force driving the binding process appears to be van der Waals interactions. The various nonelectrostatic terms can also indirectly modulate the electrostatic interactions through fine-tuning the binding pose of the ligand in the binding site, providing an explanation of why the binding specificity of nicotine to the brain versus muscle nAChRs is driven by electrostatic interaction, given that the immediate binding site residues, including the key tryptophan residue, are identical in the two receptors.
MeSH term(s)	Nicotine/chemistry ; Nicotine/metabolism ; Acetylcholine/chemistry ; Ligands ; Carrier Proteins/chemistry ; Static Electricity ; Tryptophan/chemistry ; Models, Molecular ; Receptors, Nicotinic/chemistry ; Binding Sites ; Protein Binding
Chemical Substances	Nicotine (6M3C89ZY6R) ; Acetylcholine (N9YNS0M02X) ; Ligands ; Carrier Proteins ; Tryptophan (8DUH1N11BX) ; Receptors, Nicotinic
Language	English
Publishing date	2022-10-19
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.2c04641
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Advanced Diffusion MRI of the Visual System in Glaucoma: From Experimental Animal Models to Humans

Mendoza, Monica / Shotbolt, Max / Faiq, Muneeb A. / Parra, Carlos / Chan, Kevin C.

Biology. 2022 Mar. 16, v. 11, no. 3

2022

Abstract: Glaucoma is a group of ophthalmologic conditions characterized by progressive retinal ganglion cell death, optic nerve degeneration, and irreversible vision loss. While intraocular pressure is the only clinically modifiable risk factor, glaucoma may ... ...

Abstract	Glaucoma is a group of ophthalmologic conditions characterized by progressive retinal ganglion cell death, optic nerve degeneration, and irreversible vision loss. While intraocular pressure is the only clinically modifiable risk factor, glaucoma may continue to progress at controlled intraocular pressure, indicating other major factors in contributing to the disease mechanisms. Recent studies demonstrated the feasibility of advanced diffusion magnetic resonance imaging (dMRI) in visualizing the microstructural integrity of the visual system, opening new possibilities for non-invasive characterization of glaucomatous brain changes for guiding earlier and targeted intervention besides intraocular pressure lowering. In this review, we discuss dMRI methods currently used in visual system investigations, focusing on the eye, optic nerve, optic tract, subcortical visual brain nuclei, optic radiations, and visual cortex. We evaluate how conventional diffusion tensor imaging, higher-order diffusion kurtosis imaging, and other extended dMRI techniques can assess the neuronal and glial integrity of the visual system in both humans and experimental animal models of glaucoma, among other optic neuropathies or neurodegenerative diseases. We also compare the pros and cons of these methods against other imaging modalities. A growing body of dMRI research indicates that this modality holds promise in characterizing early glaucomatous changes in the visual system, determining the disease severity, and identifying potential neurotherapeutic targets, offering more options to slow glaucoma progression and to reduce the prevalence of this world’s leading cause of irreversible but preventable blindness.
Keywords	blindness ; cell death ; disease severity ; eyes ; ganglia ; glaucoma ; laboratory animals ; magnetism ; nerve tissue ; neurons ; peripheral nervous system diseases ; risk factors ; statistical analysis ; vision ; visual cortex
Language	English
Dates of publication	2022-0316
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2661517-4
ISSN	2079-7737
ISSN	2079-7737
DOI	10.3390/biology11030454
Database	NAL-Catalogue (AGRICOLA)

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