Yiming Wang

Works (16)

Updated: July 25th, 2023 21:15

2021 review

Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer's Disease, Parkinson's Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis

[Review of ]. CHEMICAL REVIEWS, 121(4), 2545–2647.

By: P. Nguyen*, A. Ramamoorthy *, B. Sahoo *, J. Zheng *, P. Faller *, J. Straub *, L. Dominguez *, J. Shea * ...

MeSH headings : Alzheimer Disease / metabolism; Alzheimer Disease / pathology; Amyloid / chemistry; Amyloid / metabolism; Amyloid beta-Peptides / chemistry; Amyloid beta-Peptides / metabolism; Amyotrophic Lateral Sclerosis / genetics; Amyotrophic Lateral Sclerosis / metabolism; Amyotrophic Lateral Sclerosis / pathology; Animals; Diabetes Mellitus, Type 2 / metabolism; Diabetes Mellitus, Type 2 / pathology; Humans; Islet Amyloid Polypeptide / chemistry; Islet Amyloid Polypeptide / metabolism; Models, Molecular; Neurodegenerative Diseases / metabolism; Neurodegenerative Diseases / pathology; Parkinson Disease / metabolism; Parkinson Disease / pathology; Protein Aggregation, Pathological; Proteostasis Deficiencies / metabolism; Superoxide Dismutase-1 / chemistry; Superoxide Dismutase-1 / metabolism; alpha-Synuclein / chemistry; alpha-Synuclein / metabolism; tau Proteins / chemistry; tau Proteins / metabolism
TL;DR: What computer, in vitro, in vivo, and pharmacological experiments tell us about the accumulation and deposition of the oligomers of the (Aβ, tau), α-synuclein, IAPP, and superoxide dismutase 1 proteins, which have been the mainstream concept underlying Alzheimer's disease, Parkinson's disease (PD), type II diabetes (T2D), and amyotrophic lateral sclerosis (ALS) research, respectively, are reviewed. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries
Added: March 29, 2021

2021 journal article

CATCH Peptides Coassemble into Structurally Heterogeneous beta-Sheet Nanofibers with Little Preference to beta-Strand Alignment

JOURNAL OF PHYSICAL CHEMISTRY B, 125(16), 4004–4015.

By: K. Wong *, Q. Shao *, Y. Wang n, D. Seroski*, R. Liu *, A. Lint*, G. Hudalla *, C. Hall n , A. Paravastu *

MeSH headings : Amino Acid Sequence; Molecular Dynamics Simulation; Nanofibers; Peptides; Protein Conformation, beta-Strand
TL;DR: Both experimental and computational results suggest that CATCH molecules coassemble into structurally heterogeneous nanofibers, which is consistent with the observations in another coassembling system, the King-Webb peptides. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries
Added: June 10, 2021

2021 journal article

De novo design of peptides that coassemble into beta sheet-based nanofibrils

SCIENCE ADVANCES, 7(36).

By: X. Xiao n, Y. Wang n, D. Seroski*, K. Wong *, R. Liu *, A. Paravastu *, G. Hudalla *, C. Hall n 

TL;DR: Computational discoveries and experimental characterizations of coassembly peptides that form β sheet–based nanofibrils suggest that the polyene-like structure dominates in peptide-like structures while in the case of nanoporous materials, the polymethine-based structure is preferred. (via Semantic Scholar)
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Added: September 27, 2021

2021 journal article

Engineering β-Sheet Peptide Coassemblies for Biomaterial Applications

The Journal of Physical Chemistry B, 125(50), 13599–13609.

By: K. Wong *, A. Robang *, A. Lint*, Y. Wang n, X. Dong n, X. Xiao n, D. Seroski*, R. Liu * ...

MeSH headings : Biocompatible Materials; Magnetic Resonance Spectroscopy; Nanostructures; Peptides; Protein Conformation, beta-Strand
TL;DR: This perspective highlights recent advances and key challenges to understanding and controlling peptide coassembly and reveals that preconceived notions of structure and molecular organization are not always correct. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries, Crossref
Added: January 3, 2022

2020 journal article

Anatomy of a selectively coassembled beta-sheet peptide nanofiber

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 117(9), 4710–4717.

By: Q. Shao n, K. Wong *, D. Seroski*, Y. Wang n, R. Liu *, A. Paravastu *, G. Hudalla *, C. Hall n 

author keywords: coassembly; peptides; fibril; beta-barrel; coarse-grained simulation
MeSH headings : Amyloid / chemistry; Computer Simulation; Nanofibers / chemistry; Polymerization; Protein Conformation, beta-Strand; Protein Multimerization; Static Electricity
TL;DR: This work reports a computational and experimental approach to characterize molecular-level organization of the established peptide pair, CATCH, and demonstrates that strictly alternating arrangements of β-strands predominate in coassembled CATCH structures, but deviations from perfect alternation occur. (via Semantic Scholar)
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Added: March 30, 2020

2020 journal article

Development of a coarse-grained lipid model, LIME 2.0, for DSPE using multistate iterative Boltzmann inversion and discontinuous molecular dynamics simulations

FLUID PHASE EQUILIBRIA, 521.

By: K. Wang n, Y. Wang n & C. Hall n 

author keywords: Coarse-graining; Multi-state iterative Boltzmann inversion; Multiple square well; Discontinuous molecular dynamics; simulation; Lipid bilayer
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Sources: Web Of Science, NC State University Libraries
Added: September 7, 2020

2020 journal article

Molecular complementarity and structural heterogeneity within co-assembled peptide beta-sheet nanofibers

NANOSCALE, 12(7), 4506–4518.

By: K. Wong *, Y. Wang n, D. Seroski*, G. Larkin*, A. Mehta *, G. Hudalla *, C. Hall n , A. Paravastu *

MeSH headings : Nanofibers / chemistry; Peptides / chemistry; Protein Conformation, beta-Strand; Spectroscopy, Fourier Transform Infrared
TL;DR: Through a combination of solid-state NMR measurements and discontinuous molecular dynamics simulations, this work investigates the molecular organization of King-Webb peptide nanofibers and highlights structural disorder at the molecular level in a charge-complementary peptide system with implications on co-assembling peptide designs. (via Semantic Scholar)
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Added: May 26, 2020

2020 journal article

Structural insights into peptide self-assembly using photo-induced crosslinking experiments and discontinuous molecular dynamics

AICHE JOURNAL, 67(3).

By: S. Bunce *, Y. Wang n, S. Radford *, A. Wilson * & C. Hall n 

author keywords: amyloid‐ forming peptide; discontinuous molecular dynamics; peptide self assembly; photo‐ induced crosslinking
TL;DR: Detailed structural insights are provided into the Aβ16‐22 self‐ assembly processes, paving the way to explore the self‐assembly mechanism of larger, more complex peptides, including those whose aggregation is responsible for human disease. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries
Added: November 24, 2020

2019 journal article

Differential Misfolding Properties of Glaucoma-Associated Olfactomedin Domains from Humans and Mice

BIOCHEMISTRY, 58(13), 1718–1727.

By: A. Patterson-Orazem *, S. Hill *, Y. Wang n, I. Dominic *, C. Hall n  & R. Lieberman *

MeSH headings : Amyloid / chemistry; Amyloid / genetics; Animals; Crystallography, X-Ray; Cytoskeletal Proteins / chemistry; Cytoskeletal Proteins / genetics; Extracellular Matrix Proteins / chemistry; Eye Proteins / chemistry; Eye Proteins / genetics; Glaucoma / genetics; Glycoproteins / chemistry; Glycoproteins / genetics; Humans; Mice; Models, Molecular; Point Mutation; Protein Aggregates; Protein Conformation; Protein Domains; Protein Folding; Protein Stability
TL;DR: Simulations and experiments support the interpretation that kinetics of mouse OLF are faster because of a decreased charge repulsion arising from more neutral surface electrostatics, which would alter the lifetime of putatively toxic protofibrillar intermediates. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries
Added: April 22, 2019

2019 journal article

Molecular insights into the surface-catalyzed secondary nucleation of amyloid-beta(40) (A beta(40)) by the peptide fragment A beta(16-22)

SCIENCE ADVANCES, 5(6).

By: S. Bunce *, Y. Wang n, K. Stewart *, A. Ashcroft *, S. Radford *, C. Hall n , A. Wilson *

MeSH headings : Amino Acid Motifs; Amyloid beta-Peptides / chemistry; Amyloid beta-Peptides / metabolism; Catalysis; Dimerization; Kinetics; Molecular Dynamics Simulation; Peptide Fragments / chemistry; Peptide Fragments / metabolism; Protein Structure, Tertiary; Surface Properties
TL;DR: Analysis of the co-aggregation of Aβ40 and Aβ16–22, two widely studied peptide fragments implicated in Alzheimer’s disease, reveals a structural mechanism of surface-catalyzed nucleation in Aβ amyloid formation that may facilitate development of surfaces designed to enhance or suppress secondary nucleation and hence to control the rates and products of fibril assembly. (via Semantic Scholar)
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Added: July 22, 2019

2019 journal article

Thermodynamic phase diagram of amyloid-β (16–22) peptide

Proceedings of the National Academy of Sciences, 116(6), 2091–2096.

By: Y. Wang n, S. Bunce *, S. Radford *, A. Wilson *, S. Auer * & C. Hall n 

author keywords: phase diagram; solubility; amyloid; protein aggregation; coarse-grained simulation
MeSH headings : Amyloid / chemistry; Amyloid / metabolism; Amyloid / ultrastructure; Amyloid beta-Peptides / chemistry; Amyloid beta-Peptides / metabolism; Peptide Fragments; Protein Aggregates; Protein Binding; Protein Conformation; Protein Multimerization; Solubility; Thermodynamics
TL;DR: The results reveal that the only thermodynamically stable phases are the solution phase and the macroscopic fibrillar phase, and that there also exists a hierarchy of metastable phases. (via Semantic Scholar)
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Sources: Web Of Science, Crossref, NC State University Libraries
Added: February 18, 2019

2018 journal article

Seeding and cross-seeding fibrillation of N-terminal prion protein peptides PrP(120-144)

Protein Science, 27(7), 1304–1313.

By: Y. Wang n & C. Hall n 

author keywords: coarse-grained molecular dynamics; cross-seeding aggregation; prion protein fragments; amyloid formation; fibril elongation
MeSH headings : Amyloid / chemistry; Animals; Arvicolinae; Circular Dichroism; Humans; Hydrophobic and Hydrophilic Interactions; Kinetics; Mesocricetus; Models, Molecular; Molecular Dynamics Simulation; Peptide Fragments / chemistry; Prion Proteins / chemistry; Protein Structure, Secondary
TL;DR: Light is shed on the molecular mechanism of seed‐templating aggregation of prion protein fragments underlying the sequence‐dependent transmission barrier in prion diseases. (via Semantic Scholar)
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Sources: Web Of Science, Crossref, NC State University Libraries
Added: August 6, 2018

2018 journal article

Simulations and Experiments Delineate Amyloid Fibrilization by Peptides Derived from Glaucoma-Associated Myocilin

JOURNAL OF PHYSICAL CHEMISTRY B, 122(22), 5845–5850.

By: Y. Wang n, Y. Gao *, S. Hill *, D. Huard *, M. Tomlin*, R. Lieberman *, A. Paravastu *, C. Hall n 

MeSH headings : Amino Acid Sequence; Amyloid / metabolism; Cytoskeletal Proteins / chemistry; Cytoskeletal Proteins / metabolism; Eye Proteins / chemistry; Eye Proteins / metabolism; Glaucoma, Open-Angle / metabolism; Glaucoma, Open-Angle / pathology; Glycoproteins / chemistry; Glycoproteins / metabolism; Humans; Molecular Dynamics Simulation; Nuclear Magnetic Resonance, Biomolecular; Peptides / chemistry; Peptides / metabolism; Protein Aggregates / physiology; Protein Conformation, beta-Strand
TL;DR: DMD/PRIME20 simulations provide a viable method to predict peptide aggregation propensities and aggregate structure/order which cannot be accessed by bioinformatics or readily attained experimentally. (via Semantic Scholar)
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Added: August 6, 2018

2017 journal article

Aggregation of Aβ(17–36) in the Presence of Naturally Occurring Phenolic Inhibitors Using Coarse-Grained Simulations

Journal of Molecular Biology, 429(24), 3893–3908.

By: Y. Wang n, D. Latshaw  n & C. Hall n 

author keywords: discontinuous molecular dynamics; protein aggregation; polyphenol; amyloid beta; inhibitory mechanism
MeSH headings : Amyloid beta-Peptides / chemistry; Anti-Inflammatory Agents, Non-Steroidal / pharmacology; Antioxidants / pharmacology; Benzaldehydes / pharmacology; Catechin / analogs & derivatives; Catechin / pharmacology; Curcumin / pharmacology; Hydrophobic and Hydrophilic Interactions; Molecular Dynamics Simulation; Protein Aggregates / drug effects; Resveratrol; Stilbenes / pharmacology
TL;DR: D discontinuous molecular dynamics combined with the PRIME20 force field and a newly built inhibitor model are performed to examine the effect of vanillin, resveratrol, curcumin, and epigallocatechin-3-gallate (EGCG) on the aggregation of Aβ(17-36) peptides, providing molecular-level insights into how polyphenols inhibit Aβ fibril formation. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries, Crossref
Added: August 6, 2018

2017 journal article

Extended Concerted Rotation Technique Enhances the Sampling Efficiency of the Computational Peptide-Design Algorithm

JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 13(11), 5709–5720.

By: X. Xiao n, Y. Wang n, J. Leonard * & C. Hall n 

MeSH headings : Algorithms; Molecular Dynamics Simulation; Peptides / chemistry
TL;DR: Three of the evolved peptides, viz. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018

2016 journal article

N-terminal Prion Protein Peptides (PrP(120-144)) Form Parallel In-register beta-Sheets via Multiple Nucleation-dependent Pathways

JOURNAL OF BIOLOGICAL CHEMISTRY, 291(42), 22093–22105.

By: Y. Wang n, Q. Shao n & C. Hall n 

author keywords: fibril; kinetics; prion disease; protein aggregation; thermodynamics; amino acid substitution; amyloid core; discontinuous molecular dynamics
MeSH headings : Amyloid / chemistry; Animals; Arvicolinae; Cricetinae; Humans; Mesocricetus; PrPC Proteins / chemistry; Protein Aggregates; Protein Structure, Secondary
TL;DR: Light is shed on the amyloid core structures underlying prion strains and how I138M, I139M, and S143N affect prion protein aggregation kinetics. (via Semantic Scholar)
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Added: August 6, 2018

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