Works (20)
Updated: January 22nd, 2024 08:12
2024 article
Structural determination of a full-length plant cellulose synthase informed by experimental and in silico methods
Kwansa, A. L., Singh, A., Williams, J. T., Haigler, C. H., Roberts, A. W., & Yingling, Y. G. (2024, January 6). CELLULOSE, Vol. 1.
author keywords: Plant cellulose synthesis; Protein homology model; Molecular dynamics simulation; Hydrogen bonding; Gossypium hirsutum
Sources: Web Of Science, NC State University Libraries
Added: January 16, 2024
2022 article
Evidence for Plant-Conserved Region Mediated Trimeric CESAs in Plant Cellulose Synthase Complexes br
Du, J., Vandavasi, V. G., Molloy, K. R., Yang, H., Massenburg, L. N., Singh, A., … Nixon, B. T. (2022, August 10). BIOMACROMOLECULES, Vol. 8.
MeSH headings : Arabidopsis / genetics; Arabidopsis Proteins; Cell Wall; Cellulose; Glucosyltransferases / chemistry; Glucosyltransferases / genetics
TL;DR:
Inter-subunit lysine-crosslinks that localize to the small P-CR, negative-stain EM structure, and modeling data for homotrimers of AtCESA1CatD suggest that homomeric CESA trimers may be important for the synthesis of primary and secondary cell walls and identify key residues for future mutagenic studies.
(via Semantic Scholar)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 11, 2022
2021 journal article
Assessment of AMBER Force Fields for Simulations of ssDNA
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 17(2), 1208–1217.
MeSH headings : DNA, Single-Stranded / chemistry; Fluorescence Resonance Energy Transfer; Models, Chemical; Nuclear Magnetic Resonance, Biomolecular / methods; Nucleic Acid Conformation; Scattering, Small Angle; X-Ray Diffraction
TL;DR:
Assessment of existing Amber force fields for all-atom simulations of ssDNA in implicit and explicit solvents finds that some force fields agree better with experiments than others mainly due to the difference in parameterization of the propensity for hydrogen bonding and base stacking.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
7. Affordable and Clean Energy
(OpenAlex)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: January 15, 2021
2021 journal article
Phenotypic effects of changes in the FTVTxK region of an Arabidopsis secondary wall cellulose synthase compared with results from analogous mutations in other isoforms
PLANT DIRECT, 5(8).
author keywords: AtCesA7; cellulose synthesis complex; genetic complementation; irx3-1 mutant; PpCesA5; protein engineering; sum frequency generation spectroscopy
TL;DR:
The cumulative results show that the FTVTxK region is important for the function of an angiosperm secondary wall CesA as well as widely divergent primary wall CesAs, while differences in complementation results between isomers may reflect functional differences that can be explored in further work.
(via Semantic Scholar)
open access via onlinelibrary.wiley.com (publisher PDF)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2021
2021 journal article
Weakly Ionically Bound Thermosensitive Hyperbranched Polymers
LANGMUIR, 37(9), 2913–2927.
TL;DR:
It is suggested that, in contrast to traditional branched polymers, ionically linked PNIPAM macrocations can reversibly disassociate from the sulfonate groups and form mobile coronas, endowing the dynamic micellar morphologies.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
6. Clean Water and Sanitation
(Web of Science; OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: April 12, 2021
2018 journal article
Bathophenanthroline Disulfonate Ligand-Induced Self-Assembly of Ir(III) Complexes in Water: An Intriguing Class of Photoluminescent Soft Materials
ACS Omega, 3(10), 14027–14038.
Contributors: M. McGoorty n, n, T. Deaton n, B. Peterson n, C. Taliaferro n, Y. Yingling n , F. Castellano n
TL;DR:
A combination of nanoscale particle characterization techniques, static and dynamic photoluminescence spectroscopic studies, along with atomistic molecular dynamics simulations of these soft materials suggests the formation of small, heterogeneous nanoaggregate structures, wherein the sulfonated diimine ancillary ligand serves as a pro-aggregating subunit in all instances.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
6. Clean Water and Sanitation
(OpenAlex)
7. Affordable and Clean Energy
(Web of Science)
Sources: Web Of Science, Crossref, ORCID, NC State University Libraries
Added: November 26, 2018
2018 journal article
Cellulose synthase "class specific regions' are intrinsically disordered and functionally undifferentiated
JOURNAL OF INTEGRATIVE PLANT BIOLOGY, 60(6), 481–497.
Contributors: T. Scavuzzo-Duggan *, A. Chaves *, n, L. Sethaphong n, E. Slabaugh n, Y. Yingling n , C. Haigler n , A. Roberts *
MeSH headings : Amino Acid Sequence; Bryopsida / enzymology; Cellulose / metabolism; Gene Knockout Techniques; Genetic Complementation Test; Genetic Vectors / metabolism; Glucosyltransferases / chemistry; Glucosyltransferases / classification; Intrinsically Disordered Proteins / chemistry; Intrinsically Disordered Proteins / metabolism; Isoenzymes / chemistry; Isoenzymes / metabolism; Models, Molecular; Phylogeny
TL;DR:
Sequence analysis and computational modeling showed that the CSR is intrinsically disordered and contains predicted molecular recognition features, consistent with a possible role in CESA oligomerization and explaining the evolution of class-specific sequences without selection for class- specific function.
(via Semantic Scholar)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2018 journal article
Progress in ligand design for monolayer-protected nanoparticles for nanobio interfaces
Biointerphases, 13(6), 06D502.
Contributors: M. Manning n, A. Kwansa n, T. Oweida n, J. Peerless n, n & Y. Yingling n
MeSH headings : Drug Carriers / chemistry; Humans; Nanomedicine / economics; Nanomedicine / methods; Nanomedicine / trends; Nanoparticles / chemistry; Surface Properties; Technology, Pharmaceutical / economics; Technology, Pharmaceutical / methods; Technology, Pharmaceutical / trends
TL;DR:
A comprehensive understanding of ligand design principles lies in the cost associated with synthesizing and characterizing diverse ligand chemistries and the ability to carefully assess the structural integrity of biomolecules upon interactions with nanoparticles.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, Crossref, ORCID, NC State University Libraries
Added: December 3, 2018
2016 journal article
Comparative Structural and Computational Analysis Supports Eighteen Cellulose Synthases in the Plant Cellulose Synthesis Complex
Scientific Reports, 6(1).
Contributors: B. Nixon *, K. Mansouri n, n, J. Du *, J. Davis n, J. Lee n, E. Slabaugh n, V. Vandavasi *
MeSH headings : Cellulose / biosynthesis; Cellulose / chemistry; Glucosyltransferases / chemistry; Models, Molecular; Plant Proteins / chemistry; Protein Domains; Protein Folding; Protein Structure, Quaternary
TL;DR:
Improved transmission electron microscopy images and image averages of the rosette-type CSC are obtained, revealing the frequent triangularity and average cross-sectional area in the plasma membrane of its individual lobes and multifaceted data support a rosettes CSC with 18 CESAs that mediates the synthesis of a fundamental microfibril composed of 18 glucan chains.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy
(OpenAlex)
Sources: Web Of Science, ORCID, NC State University Libraries, Crossref
Added: August 6, 2018
2015 journal article
A Barley Efflux Transporter Operates in a Na+-Dependent Manner, as Revealed by a Multidisciplinary Platform
Plant Cell, 28(1), 202–218.
Contributors: Y. Nagarajan*, J. Rongala*, S. Luang*, n, N. Shadiac*, J. Hayes *, T. Sutton *, M. Gilliham *
MeSH headings : Anions / metabolism; Binding Sites; Borates / metabolism; Cell-Free System; Computer Simulation; Hordeum / metabolism; Lipid Bilayers / metabolism; Liposomes / metabolism; Membrane Transport Proteins / chemistry; Membrane Transport Proteins / metabolism; Models, Molecular; Permeability; Pichia / metabolism; Plant Proteins / chemistry; Plant Proteins / metabolism; Protein Folding; Protein Multimerization; Sodium / metabolism; Triticum / metabolism
TL;DR:
Using alanine scanning, molecular dynamics simulations, and transport measurements, it is shown that conductance by Bot1 is abolished by removal of the Na+ ion binding site, which enhances the understanding of the permeation functions of Bot1.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
15. Life on Land
(OpenAlex)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2015 journal article
CELLULOSE SYNTHASE INTERACTIVE1 Is Required for Fast Recycling of Cellulose Synthase Complexes to the Plasma Membrane in Arabidopsis
The Plant Cell, 27(10), tpc.15.00442.
Contributors: L. Lei *, n, L. Bashline*, S. Li *, Y. Yingling n & Y. Gu *
MeSH headings : Arabidopsis / genetics; Arabidopsis / physiology; Arabidopsis / ultrastructure; Arabidopsis Proteins / genetics; Arabidopsis Proteins / metabolism; Carrier Proteins / genetics; Carrier Proteins / metabolism; Cell Membrane / enzymology; Cellulose / metabolism; Clathrin / metabolism; Endocytosis; Genes, Reporter; Glucosyltransferases / genetics; Glucosyltransferases / metabolism; Microtubules / metabolism; Models, Molecular; Protein Transport; Seedlings / genetics; Seedlings / physiology; Seedlings / ultrastructure
TL;DR:
This study establishes a model in which CSI1-dependent SmaCCs/MASCs are formed through a process that involves endocytosis, which represents an important mechanism for plants to quickly regulate cellulose synthesis under abiotic stress.
(via Semantic Scholar)
Sources: Web Of Science, ORCID, NC State University Libraries, Crossref
Added: August 6, 2018
2015 journal article
Characterization of Nucleic Acid Compaction with Histone-Mimic Nanoparticles through All-Atom Molecular Dynamics
ACS NANO, 9(12), 12374–12382.
Contributors: Y. Yingling n , N. Li n, n & J. Nash n
author keywords: gold nanoparticles; DNA compaction; RNA compaction; molecular dynamics simulations; nanoparticle binding; nucleosome
MeSH headings : Gold / chemistry; Histones / chemistry; Metal Nanoparticles / chemistry; Molecular Dynamics Simulation; Nucleic Acids / chemistry; Nucleic Acids / metabolism; Nucleic Acids / ultrastructure
TL;DR:
Large-scale, all-atom simulations of ligand-functionalized gold nanoparticle (NP) binding to double stranded NAs as a function of NP charge and solution salt concentration reveal different responses of RNA and DNA to cationic NPs.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2015 journal article
Prediction of the structures of the plant-specific regions of vascular plant cellulose synthases and correlated functional analysis
Cellulose, 23(1), 145–161.
Contributors: Y. Yingling n , C. Haigler n , n, E. Slabaugh n, J. Davis n & L. Sethaphong n
author keywords: Arabidopsis thaliana; Cellulose synthesis; Computational protein structure prediction; Isoform specificity; Mutant complementation
TL;DR:
Modeling of the mutant P-CR of Atcesa8R362K (fra6) suggested that changes in local structural stability and surface electrostatics may cause the mutant phenotype, and results provide structural clues about the function of plant-specific regions of CESA.
(via Semantic Scholar)
Sources: Web Of Science, ORCID, NC State University Libraries, Crossref
Added: August 6, 2018
2012 journal article
The effect of point mutations on structure and mechanical properties of collagen-like fibril: A molecular dynamics study
MATERIALS SCIENCE & ENGINEERING C-MATERIALS FOR BIOLOGICAL APPLICATIONS, 32(8), 2583–2588.
Contributors: A. Marlowe n, n & Y. Yingling n
author keywords: Collagen fibril; Molecular dynamics simulations; Point mutations; Osteogenesis Imperfecta; Mechanical properties
TL;DR:
The results suggest that the reduction in mechanical properties of collagen fibrils may be used to predict the clinical outcome of mutations, as well as the trend in reduction of fibril's tensile strength predicted by simulations.
(via Semantic Scholar)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2012 journal article
Weakly Charged Cationic Nanoparticles Induce DNA Bending and Strand Separation
ADVANCED MATERIALS, 24(31), 4261-+.
Contributors: J. Railsback n, n, R. Pearce n, T. McKnight *, R. Collazo n , Z. Sitar n, Y. Yingling n , A. Melechko n
author keywords: gold nanoparticles; DNA compaction; DNA denaturing; cationic ligands; DNA-nanoparticle interactions
MeSH headings : Cations / chemistry; DNA / chemistry; Gold / chemistry; Molecular Dynamics Simulation; Nanoparticles / chemistry; Nucleic Acid Conformation; Nucleic Acid Denaturation; Spectrophotometry, Ultraviolet
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2011 journal article
Interactions of Cations with RNA Loop-Loop Complexes
BIOPHYSICAL JOURNAL, 101(3), 727–735.
Contributors: n, L. Sethaphong n & Y. Yingling n
MeSH headings : Base Pairing; Base Sequence; Cations / metabolism; Metals / metabolism; Molecular Dynamics Simulation; Nucleic Acid Conformation; RNA / chemistry; RNA / genetics; RNA / metabolism; Solvents / chemistry
TL;DR:
Examining interactions of metal ions with five RNA loop-loop complexes of unique biological significance using explicit-solvent molecular-dynamics simulations revealed the presence of solvent-accessible tunnels through the major groove of loop- loop interactions that attract and retain cations.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2011 article
Theoretical Perspective on Properties of DNA-Functionalized Surfaces
Singh, A., Eksiri, H., & Yingling, Y. G. (2011, November 15). JOURNAL OF POLYMER SCIENCE PART B-POLYMER PHYSICS, Vol. 49, pp. 1563–1568.
Contributors: Y. Yingling n , H. Eksiri n & n
author keywords: DNA-functionalized surface; modeling; nanotechnology; simulations; theory
TL;DR:
The understanding of structure and dynamics of DNA immobilized on the surfaces from the theoretical point of view including recent progress in analytical theories, atomistic simulations, and coarse-grained models is discussed.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2011 article
X3DBio1: A Visual Analysis Tool for Biomolecular Structure Exploration
(P. C. Wong, D. L. Kao, M. C. Hao, C. Chen, R. Kosara, M. A. Livingston, … I. Roberts, Eds.). VISUALIZATION AND DATA ANALYSIS 2012, Vol. 8294.
Ed(s): P. Wong, D. Kao, M. Hao, C. Chen, R. Kosara, M. Livingston, J. Park, I. Roberts
author keywords: molecular visualization; visual analytics; interactive exploration; protein structure; contact map
TL;DR:
X3DBio1, a visual analysis tool for 3D biomolecular structure exploration, which allows for easy visual analysis of 2D intra-molecular contact map and 3D density exploration for protein, DNA, and RNA structures, is presented.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2010 journal article
Effect of Oligonucleotide Length on the Assembly of DNA Materials: Molecular Dynamics Simulations of Layer-by-Layer DNA Films
LANGMUIR, 26(22), 17339–17347.
Contributors: Y. Yingling n , F. Caruso *, A. Johnston *, L. Lee *, S. Snyder n & n
MeSH headings : Base Sequence; DNA / chemistry; DNA / genetics; Gold / chemistry; Metal Nanoparticles / chemistry; Molecular Dynamics Simulation; Nanotechnology / methods; Nucleic Acid Conformation; Nucleic Acid Hybridization; Oligodeoxyribonucleotides / chemistry; Oligodeoxyribonucleotides / genetics; Poly T / chemistry; Quartz Crystal Microbalance Techniques
TL;DR:
This study suggests that restrainedpolyT, compared to labile suspensions of free polyT, are more capable of hybridization and hence DNA-based assembly, and this can be associated with the limited accessibility of the bases on the surface due to formation of self-protected interactions that prevent efficient hybridization.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2010 journal article
The Sequence of HIV-1 TAR RNA Helix Controls Cationic Distribution
JOURNAL OF PHYSICAL CHEMISTRY C, 114(12), 5506–5512.
Contributors: Y. Yingling n , A. Marlowe n, n & L. Sethaphong n
TL;DR:
There is a sequence-dependent cationic localization toward the purine-rich run within the TAR helix and other purine -rich duplexes and the behavior is independent of ionic species or a presence of a bulge.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
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