Research Output 1960 2019

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2019

1 H-decoupling and Isotopic Labeling for the Measurement of the Longitudinal Relaxation Time of Hyperpolarized 13 C-Methylenes in Choline Analogs

Uppala, S., Gamliel, A., Harris, T., Sosna, J., Gomori, J. M., Jerschow, A. & Katz-Brull, R., Jan 1 2019, In : Israel Journal of Chemistry.

Research output: Contribution to journalArticle

Choline
Relaxation time
Labeling
Protons
Polarization

Ab Initio Molecular Dynamics Study of Hydroxide Diffusion Mechanisms in Nanoconfined Structural Mimics of Anion Exchange Membranes

Zelovich, T., Long, Z., Hickner, M., Paddison, S. J., Bae, C. & Tuckerman, M., Feb 28 2019, In : Journal of Physical Chemistry C. 123, 8, p. 4638-4653 16 p.

Research output: Contribution to journalArticle

hydroxides
Anions
Molecular dynamics
Ion exchange
Negative ions

A Biomimetic Synthesis Elucidates the Origin of Preuisolactone A

Novak, A. J. E., Grigglestone, C. E. & Trauner, D., Jan 1 2019, (Accepted/In press) In : Journal of the American Chemical Society.

Research output: Contribution to journalArticle

Polyketides
Biomimetics
Cycloaddition
Cycloaddition Reaction
Metabolites

Accelerated Molecular Dynamics Simulation for Helical Proteins Folding in Explicit Water

Duan, L., Guo, X., Cong, Y., Feng, G., Li, Y. & Zhang, J., Aug 6 2019, In : Frontiers in Chemistry. 7, 540.

Research output: Contribution to journalArticle

Open Access
Protein folding
Molecular dynamics
Water
Computer simulation
Temperature
entropy
Free energy
Permittivity
Entropy
Proteins

A Conserved Allosteric Pathway in Tyrosine Kinase Regulation

Marsiglia, W. M., Katigbak, J., Zheng, S., Mohammadi, M., Zhang, Y. & Traaseth, N. J., Aug 6 2019, In : Structure. 27, 8, p. 1308-1315.e3

Research output: Contribution to journalArticle

Isoleucine
Phenylalanine
Protein-Tyrosine Kinases
Phosphotransferases
Mutation

A force consistent method for electrostatic energy calculation in fluctuating charge model

Duan, G., Ji, C. & Zhang, J., Sep 7 2019, In : Journal of Chemical Physics. 151, 9, 094105.

Research output: Contribution to journalArticle

Open Access
Electrostatics
electrostatics
energy
Coulomb interactions
Molecular dynamics

A Fragment Quantum Mechanical Method for Metalloproteins

Xu, M., He, X., Zhu, T. & Zhang, J., Jan 1 2019, (Accepted/In press) In : Journal of Chemical Theory and Computation.

Research output: Contribution to journalArticle

Metalloproteins
Potential energy
potential energy
fragments
Structural optimization

Altered steady state and activity-dependent de novo protein expression in fragile X syndrome

Bowling, H., Bhattacharya, A., Zhang, G., Alam, D., Lebowitz, J. Z., Bohm-Levine, N., Lin, D., Singha, P., Mamcarz, M., Puckett, R., Zhou, L., Aryal, S., Sharp, K., Kirshenbaum, K., Berry-Kravis, E., Neubert, T. A. & Klann, E., Dec 1 2019, In : Nature Communications. 10, 1, 1710.

Research output: Contribution to journalArticle

Open Access
Fragile X Syndrome
proteins
Blood
blood
mice

An extended dual graph library and partitioning algorithm applicable to pseudoknotted RNA structures

Jain, S., Saju, S., Petingi, L. & Schlick, T., Jan 1 2019, In : Methods.

Research output: Contribution to journalArticle

Libraries
RNA
Topology
Nucleic Acid Databases
Graph theory

Assembly and Dynamic Analysis of Square Colloidal Crystals via Templated Capillary Assembly

Shillingford, C., Grebe, V., McMullen, A., Brujic, J. & Weck, M., Sep 17 2019, In : Langmuir. 35, 37, p. 12205-12214 10 p.

Research output: Contribution to journalArticle

Optical lattices
Osmosis
osmosis
Polymethyl Methacrylate
Sols

Assessment of the Silver Penetration and Distribution in Carious Lesions of Deciduous Teeth Treated with Silver Diamine Fluoride

Li, Y., Liu, Y., Psoter, W. J., Nguyen, O. M., Bromage, T., Walters, M., Hu, B., Rabieh, S. & Kumararaja, F. C., Jan 1 2019, In : Caries Research.

Research output: Contribution to journalArticle

Deciduous Tooth
Silver
X-Ray Emission Spectrometry
Dental Enamel
Electron Scanning Microscopy

Atomic structures of RNA nanotubes and their comparison with DNA nanotubes

Naskar, S., Joshi, H., Chakraborty, B., Seeman, N. C. & Maiti, P. K., Aug 21 2019, In : Nanoscale. 11, 31, p. 14863-14878 16 p.

Research output: Contribution to journalArticle

RNA
Drug delivery
Nanotubes
Molecular dynamics
DNA

BAR-based optimum adaptive steered MD for configurational sampling

Wang, X., Tu, X., Deng, B., Zhang, J. & Sun, Z., Jan 1 2019, In : Journal of Computational Chemistry.

Research output: Contribution to journalArticle

Surface mount technology
Sampling
Adaptive Sampling
Free energy
Adaptive Method
Tacrolimus Binding Proteins
Technology
Molecular Dynamics Simulation
Steroid Receptors
Drug Design

Biomimetic Approach Toward Enterocin and Deoxyenterocin

Rizzo, A., Mayer, R. J. & Trauner, D., Feb 1 2019, In : Journal of Organic Chemistry. 84, 3, p. 1162-1175 14 p.

Research output: Contribution to journalArticle

Biomimetics
Biological Products
Polyketides
Ketones
Discrete Fourier transforms

Body Mass Index in Multiple Sclerosis modulates ceramide-induced DNA methylation and disease course

Castro, K., Ntranos, A., Amatruda, M., Petracca, M., Kosa, P., Chen, E. Y., Morstein, J., Trauner, D., Watson, C. T., Kiebish, M. A., Bielekova, B., Inglese, M., Katz Sand, I. & Casaccia, P., Jan 1 2019, In : EBioMedicine.

Research output: Contribution to journalArticle

Open Access
Ceramides
DNA Methylation
Multiple Sclerosis
Body Mass Index
Genes

Chiroptical Differentiation of Twisted Chiral and Achiral Polymer Crystals

Ye, H. M., Freudenthal, J. H., Tan, M., Yang, J. & Kahr, B., Jan 1 2019, In : Macromolecules.

Research output: Contribution to journalArticle

Polymers
Crystals
Light polarization
Crystalline materials
Scanning probe microscopy

Cobalt-Catalyzed Intramolecular Silylperoxidation of Unsaturated Diisopropylsilyl Ethers

Oswald, J. P. & Woerpel, K., Jun 21 2019, In : Journal of Organic Chemistry. 84, 12, p. 7564-7574 11 p.

Research output: Contribution to journalArticle

Acetals
Ethers
Peroxides
Cobalt

Colloidal Organosilica Spheres for Three-Dimensional Confocal Microscopy

Liu, Y., Yanagishima, T., Curran, A., Edmond, K. V., Sacanna, S. & Dullens, R. P. A., Jun 18 2019, In : Langmuir. 35, 24, p. 7962-7969 8 p.

Research output: Contribution to journalArticle

Confocal microscopy
microscopy
Optical tweezers
Polydispersity
Phase behavior

Combining Iteration-Free Polarization with Large Time Step Stochastic-Isokinetic Integration

Albaugh, A., Tuckerman, M. & Head-Gordon, T., Apr 9 2019, In : Journal of Chemical Theory and Computation. 15, 4, p. 2195-2205 11 p.

Research output: Contribution to journalArticle

iteration
self consistent fields
Molecular dynamics
Polarization
Potential energy surfaces

Compartmentalized Nanoreactors for One-Pot Redox-Driven Transformations

Qu, P., Kuepfert, M., Jockusch, S. & Weck, M., Jan 1 2019, In : ACS Catalysis. p. 2701-2706 6 p.

Research output: Contribution to journalArticle

Nanoreactors
Micelles
Alcohols
Ketones
Catalysts

Computational analysis for residue-specific CDK2-inhibitor bindings

Yang, Y. P., He, L. P., Bao, J. X., Qi, Y. F. & Zhang, J., Feb 1 2019, In : Chinese Journal of Chemical Physics. 32, 1, p. 134-142 9 p.

Research output: Contribution to journalArticle

Open Access
Cyclin-Dependent Kinase 2
inhibitors
Free energy
cancer
Cells

Computational analysis of hot spots and binding mechanism in the PD-1/PD-L1 interaction

Huang, D., Wen, W., Liu, X., Li, Y. & Zhang, J., Jan 1 2019, In : RSC Advances. 9, 26, p. 14944-14956 13 p.

Research output: Contribution to journalArticle

Open Access
Tumors
Proteins
Programmed Cell Death 1 Receptor
Cells
Monoclonal antibodies

Concise Asymmetric Synthesis of Kweichowenol A

Konrad, D. B., Kicin, B. & Trauner, D., Jan 1 2019, In : Synlett. 30, 4, p. 383-386 4 p.

Research output: Contribution to journalArticle

Open Access
Biological Products
Oxygenation
3-hydroxybutanal
cyclohexene
Molecular Dynamics Simulation
Principal Component Analysis

DeepDDG: Predicting the Stability Change of Protein Point Mutations Using Neural Networks

Cao, H., Wang, J., He, L., Qi, Y. & Zhang, J., Apr 22 2019, In : Journal of Chemical Information and Modeling. 59, 4, p. 1508-1514 7 p.

Research output: Contribution to journalArticle

neural network
Neural networks
Proteins
engineering
determinants

Designing Higher Resolution Self-Assembled 3D DNA Crystals via Strand Terminus Modifications

Ohayon, Y. P., Hernandez, C., Chandrasekaran, A. R., Wang, X., Abdallah, H. O., Jong, M. A., Mohsen, M. G., Sha, R., Birktoft, J. J., Lukeman, P. S., Chaikin, P. M., Ginell, S. L., Mao, C. & Seeman, N. C., Jul 23 2019, In : ACS Nano. 13, 7, p. 7957-7965 9 p.

Research output: Contribution to journalArticle

nucleotides
Nucleotides
Dimers
strands
Self assembly

Determination of binding affinities of 3-Hydroxy-3-Methylglutaryl Coenzyme A reductase inhibitors from free energy calculation

Sun, Z., Wang, X. & Zhang, J., May 16 2019, In : Chemical Physics Letters. 723, p. 1-10 10 p.

Research output: Contribution to journalArticle

coenzymes
inhibitors
Free energy
affinity
Enthalpy

Determining Optimal Coarse-Grained Representation for Biomolecules Using Internal Cluster Validation Indexes

Wu, Z., Zhang, Y., Zhang, J. Z., Xia, K. & Xia, F., Jan 1 2019, (Accepted/In press) In : Journal of Computational Chemistry.

Research output: Contribution to journalArticle

Cluster Validation
Biomolecules
Internal
Coarse-graining
Silhouette

Diagnosing current distributions in batteries with magnetic resonance imaging

Mohammadi, M., Silletta, E. V., Ilott, A. J. & Jerschow, A., Dec 2019, In : Journal of Magnetic Resonance. 309, 106601.

Research output: Contribution to journalArticle

Magnetic resonance
current distribution
magnetic resonance
electric batteries
Magnetic Resonance Imaging

Diastereoselective peroxidation of derivatives of Baylis–Hillman adducts

Zuckerman, D. S. & Woerpel, K., Jan 1 2019, In : Tetrahedron.

Research output: Contribution to journalArticle

Peroxides
Lactones
Cobalt
Derivatives

Diastereoselectivities in Reductions of α-Alkoxy Ketones Are Not Always Correlated to Chelation-Induced Rate Acceleration

Bartolo, N. D., Hornstein, A. L., Zhao, A. Y. & Woerpel, K., Jan 1 2019, In : Synthesis (Germany). 51, 1, p. 296-302 7 p.

Research output: Contribution to journalArticle

Chelation
Ketones
Reducing Agents
Reducing agents
Organometallics

Dislocation generation by microparticle inclusions

Zhong, X., Shtukenberg, A. G., Liu, M., Olson, I. A., Weck, M., Ward, M. & Kahr, B., Jan 1 2019, (Accepted/In press) In : Crystal Growth and Design.

Research output: Contribution to journalArticle

microparticles
Dislocations (crystals)
inclusions
Crystals
Crystal growth from solution
Open Access
Diagnostic Imaging
Ions
Magnetic Fields
Artifacts
Technology

Drug-resistance mechanisms of three mutations in anaplastic lymphoma kinase against two inhibitors based on MM/PBSA combined with interaction entropy

Xiao, Z., Cong, Y., Huang, K., Zhong, S., Zhang, J. & Duan, L., Jan 1 2019, In : Physical Chemistry Chemical Physics. 21, 37, p. 20951-20964 14 p.

Research output: Contribution to journalArticle

mutations
inhibitors
drugs
Entropy
entropy

Dual farnesyl and geranylgeranyl transferase inhibitor thwarts mutant KRAS-driven patient-derived pancreatic tumors

Kazi, A., Xiang, S., Yang, H., Chen, L., Kennedy, P., Ayaz, M., Fletcher, S., Cummings, C., Lawrence, H. R., Beato, F., Kang, Y., Kim, M. P., Delitto, A., Underwood, P. W., Fleming, J. B., Trevino, J. G., Hamilton, A. & Sebti, S. M., Oct 1 2019, In : Clinical Cancer Research. 25, 19, p. 5984-5996 13 p.

Research output: Contribution to journalArticle

Farnesyltranstransferase
Transferases
Pancreatic Neoplasms
Heterografts
Prenylation

Effect of mutations on binding of ligands to guanine riboswitch probed by free energy perturbation and molecular dynamics simulations

Chen, J., Wang, X., Pang, L., Zhang, J. Z. H. & Zhu, T., Jul 26 2019, In : Nucleic acids research. 47, 13, p. 6618-6631 14 p.

Research output: Contribution to journalArticle

Open Access
Riboswitch
Guanine
Molecular Dynamics Simulation
Ligands
Mutation

E to Z Photoisomerization of Phytochrome Cph1ΔExceeds the Born-Oppenheimer Adiabatic Limit

Bizimana, L. A., Farfan, C. A., Brazard, J. & Turner, D., Jan 1 2019, In : Journal of Physical Chemistry Letters.

Research output: Contribution to journalArticle

phytochrome
Phytochrome
Photoisomerization
Electronic states
Excited states

Excision of Oxidatively Generated Guanine Lesions by Competing Base and Nucleotide Excision Repair Mechanisms in Human Cells

Shafirovich, V., Kropachev, K., Kolbanovskiy, M. & Geacintov, N., Jan 1 2019, In : Chemical Research in Toxicology.

Research output: Contribution to journalArticle

Guanine
DNA Repair
Repair
Nucleotides
Cells

Generation of 8-oxo-7,8-dihydroguanine in G-Quadruplexes Models of Human Telomere Sequences by One-electron Oxidation

Merta, T. J., Geacintov, N. & Shafirovich, V., Jan 1 2019, In : Photochemistry and Photobiology. 95, 1, p. 244-251 8 p.

Research output: Contribution to journalArticle

telomeres
G-Quadruplexes
Telomere
Electrons
Ions

Genetically Targeted Optical Control of an Endogenous G Protein-Coupled Receptor

Donthamsetti, P. C., Broichhagen, J., Vyklicky, V., Stanley, C., Fu, Z., Visel, M., Levitz, J. L., Javitch, J. A., Trauner, D. & Isacoff, E. Y., Jul 24 2019, In : Journal of the American Chemical Society. 141, 29, p. 11522-11530 9 p.

Research output: Contribution to journalArticle

G-Protein-Coupled Receptors
Proteins
Anchors
Membranes
Ligands
clathrates
Vibrational spectra
Hydrates
hydrates
frequency shift

Heterofunctionalized Cavitands by Macrocyclization of Sequence-Defined Foldamers

Meisel, J. W., Hu, C. T. & Hamilton, A., Oct 4 2019, In : Organic Letters. 21, 19, p. 7763-7767 5 p.

Research output: Contribution to journalArticle

Open Access
Functional groups
Bearings (structural)
Artificial Receptors
Molecular recognition
Solid-Phase Synthesis Techniques

High-throughput protein nanopatterning

Liu, X., Kumar, M., Calo, A., Albisetti, E., Zheng, X., Manning, K. B., Elacqua, E., Weck, M., Ulijn, R. V. & Riedo, E., Jan 1 2019, In : Faraday Discussions. 219, p. 33-43 11 p.

Research output: Contribution to journalArticle

enzymes
Throughput
proteins
Enzymes
Proteins

Hydrogen-bonded frameworks for molecular structure determination

Li, Y., Tang, S., Yusov, A., Rose, J., Borrfors, A. N., Hu, C. T. & Ward, M. D., Dec 1 2019, In : Nature Communications. 10, 1, 4477.

Research output: Contribution to journalArticle

Open Access
Molecular Structure
X-Ray Diffraction
Molecular structure
Hydrogen
molecular structure

Hydroxide Ion Diffusion in Anion-Exchange Membranes at Low Hydration: Insights from Ab Initio Molecular Dynamics

Zelovich, T., Vogt-Maranto, L., Hickner, M. A., Paddison, S. J., Bae, C., Dekel, D. R. & Tuckerman, M., Aug 13 2019, In : Chemistry of Materials. 31, 15, p. 5778-5787 10 p.

Research output: Contribution to journalArticle

Hydration
Anions
Molecular dynamics
Ion exchange
Negative ions

Identification and structure-function analyses of an allosteric inhibitor of the tyrosine phosphatase PTPN22

Li, K., Hou, X., Li, R., Bi, W., Yang, F., Chen, X., Xiao, P., Liu, T., Lu, T., Zhou, Y., Tian, Z., Shen, Y., Zhang, Y., Wang, J., Fang, H., Sun, J. & Yu, X., Jan 1 2019, In : Journal of Biological Chemistry. 294, 21, p. 8653-8663 11 p.

Research output: Contribution to journalArticle

Protein Tyrosine Phosphatases
Phosphatases
Phosphoric Monoester Hydrolases
Tyrosine
Allosteric Site

Inducing conformational preference of the membrane protein transporter EmrE through conservative mutations

Leninger, M., Sae Her, A. & Traaseth, N. J., Oct 22 2019, In : eLife. 8

Research output: Contribution to journalArticle

Open Access
Membrane Transport Proteins
Membrane Proteins
Multiple Drug Resistance
Dimers
Mutation

Inertial water response dominates protein solvation dynamics

Bizimana, L. A., Epstein, J. & Turner, D., Aug 1 2019, In : Chemical Physics Letters. 728, p. 1-5 5 p.

Research output: Contribution to journalArticle

Solvation
solvation
proteins
Water
water