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2018

Computational design of chemogenetic and optogenetic split proteins

Dagliyan, O., Krokhotin, A., Ozkan-Dagliyan, I., Deiters, A., Der, C. J., Hahn, K. M. & Dokholyan, N. V., Dec 1 2018, In : Nature Communications. 9, 1, 4042.

Research output: Contribution to journalArticle

protein
hypothesis testing
biological processes
ligand
prediction

G4941K substitution in the pore-lining S6 helix of the skeletal muscle ryanodine receptor increases RyR1 sensitivity to ytosolic and luminal Ca2+

Xu, L., Mowrey, D. D., Chirasani, V. R., Wang, Y., Pasek, D. A., Dokholyan, N. V. & Meissner, G. W., Jan 1 2018, In : Journal of Biological Chemistry. 293, 6, p. 2015-2028 14 p.

Research output: Contribution to journalArticle

S 6
Ryanodine Receptor Calcium Release Channel
Linings
Muscle
Skeletal Muscle
3 Citations

High-speed atomic force microscopy reveals structural dynamics of α -synuclein monomers and dimers

Zhang, Y., Hashemi, M., Lv, Z., Williams, B., Popov, K. I., Dokholyan, N. V. & Lyubchenko, Y. L., Mar 28 2018, In : Journal of Chemical Physics. 148, 12, 123322.

Research output: Contribution to journalArticle

alpha-Synuclein
dynamic structural analysis
Structural dynamics
Dimers
Atomic force microscopy
1 Citations
Amyotrophic Lateral Sclerosis
Cell Survival
Motor Neurons
Poisons
Neurodegenerative Diseases

Ligand binding to a remote site thermodynamically corrects the F508del mutation in the human cystic fibrosis transmembrane conductance regulator

Wang, C., Aleksandrov, A. A., Yang, Z., Forouhar, F., Proctor, E. A., Kota, P., An, J., Kaplan, A., Khazanov, N., Boël, G., Stockwell, B. R., Senderowitz, H., Dokholyan, N. V., Riordan, J. R., Brouillette, C. G. & Hunt, J. F., Jan 1 2018, In : Journal of Biological Chemistry. 293, 46, p. 17685-17704 20 p.

Research output: Contribution to journalArticle

Electrophysiology
Cystic Fibrosis Transmembrane Conductance Regulator
Nucleotides
Stabilization
Ligands

Mapping allosteric linkage to channel gating by extracellular domains in the human epithelial sodium channel

Shobair, M., Popov, K. I., Dang, Y. L., He, H., Jackson Stutts, M. & Dokholyan, N. V., Jan 1 2018, In : Journal of Biological Chemistry. 293, 10, p. 3675-3684 10 p.

Research output: Contribution to journalArticle

Epithelial Sodium Channels
Chromosome Mapping
Degenerin Sodium Channels
Cysteine
Chemical activation

miRNA-711 Binds and Activates TRPA1 Extracellularly to Evoke Acute and Chronic Pruritus

Han, Q., Liu, D., Convertino, M., Wang, Z., Jiang, C., Kim, Y. H., Luo, X., Zhang, X., Neely, A. G., Dokholyan, N. V. & Ji, R. R., Aug 8 2018, In : Neuron. 99, 3, p. 449-463.e6

Research output: Contribution to journalArticle

Pruritus
MicroRNAs
Lymphoma
Ion Channels
S 6

P62-dependent phase separation of patient-derived KEap1 mutations and Nrf2

Cloer, E. W., Siesser, P. F., Cousins, E. M., Goldfarb, D., Mowrey, D. D., Harrison, J. S., Weir, S. J., Dokholyan, N. V. & Major, M. B., Nov 1 2018, In : Molecular and cellular biology. 38, 22, e0064417.

Research output: Contribution to journalArticle

Autophagy
Lung Neoplasms
Oxidative Stress
Mutation
Polyubiquitin

Reversible and Tunable Photoswitching of Protein Function through Genetic Encoding of Azobenzene Amino Acids in Mammalian Cells

Luo, J., Samanta, S., Convertino, M., Dokholyan, N. V. & Deiters, A., Oct 18 2018, In : ChemBioChem. 19, 20, p. 2178-2185 8 p.

Research output: Contribution to journalArticle

Cells
Amino Acids
Firefly Luciferases
Amino Acyl-tRNA Synthetases
Proteins

RNA Fibers as Optimized Nanoscaffolds for siRNA Coordination and Reduced Immunological Recognition

Rackley, L., Stewart, J. M., Salotti, J., Krokhotin, A., Shah, A., Halman, J. R., Juneja, R., Smollett, J., Lee, L., Roark, K., Viard, M., Tarannum, M., Vivero-Escoto, J., Johnson, P. F., Dobrovolskaia, M. A., Dokholyan, N. V., Franco, E. & Afonin, K. A., Jan 1 2018, (Accepted/In press) In : Advanced Functional Materials. 1805959.

Research output: Contribution to journalArticle

immunology
Immunology
Nucleic acids
nucleic acids
RNA
2 Citations

Structural complexity and functional diversity of plant NADPH oxidases

Kaur, G., Guruprasad, K., Temple, B., Shirvanyants, D. G., Dokholyan, N. V. & Pati, P. K., Jan 1 2018, In : Amino Acids. 50, 1, p. 79-94 16 p.

Research output: Contribution to journalArticle

NADPH Oxidase
Plant Structures
Gene Duplication
Protein Folding
Molecular Dynamics Simulation
1 Citations

Tyrosine phosphorylation switching of a G protein

Li, B., Tunc-Ozdemir, M., Urano, D., Jia, H., Werth, E. G., Mowrey, D. D., Hicks, L. M., Dokholyan, N. V., Torres, M. P. & Jones, A. M., Jan 1 2018, In : Journal of Biological Chemistry. 293, 13, p. 4752-4766 15 p.

Research output: Contribution to journalArticle

Phosphorylation
GTP Phosphohydrolases
GTP-Binding Proteins
Tyrosine
GTP-Binding Protein Regulators
2017
3 Citations

A Structural Model for Vinculin Insertion into PIP2-Containing Membranes and the Effect of Insertion on Vinculin Activation and Localization

Thompson, P. M., Ramachandran, S., Case, L. B., Tolbert, C. E., Tandon, A., Pershad, M., Dokholyan, N. V., Waterman, C. M. & Campbell, S. L., Feb 7 2017, In : Structure. 25, 2, p. 264-275 12 p.

Research output: Contribution to journalArticle

Vinculin
Structural Models
Focal Adhesions
Membranes
Lipid Bilayers
2 Citations

Comparative Visualization of the RNA Suboptimal Conformational Ensemble In Vivo

Woods, C. T., Lackey, L., Williams, B., Dokholyan, N. V., Gotz, D. & Laederach, A., Jul 25 2017, In : Biophysical journal. 113, 2, p. 290-301 12 p.

Research output: Contribution to journalArticle

RNA
Acylation
Hydroxyl Radical
Adenine
Riboswitch
3 Citations

Computational protein design through grafting and stabilization

Zhu, C., Mowrey, D. D. & Dokholyan, N. V., Jan 1 2017, Methods in Molecular Biology. Humana Press Inc., p. 227-241 15 p. (Methods in Molecular Biology; vol. 1529).

Research output: Chapter in Book/Report/Conference proceedingChapter

Mutation
Proteins
Protein Stability
Software
Databases
6 Citations

Direct identification of base-paired RNA nucleotides by correlated chemical probing

Krokhotin, A., Mustoe, A. M., Weeks, K. M. & Dokholyan, N. V., Jan 1 2017, In : RNA. 23, 1, p. 6-13 8 p.

Research output: Contribution to journalArticle

Nucleotides
RNA
Base Pairing
3 Citations

Engineering Pak1 Allosteric Switches

Dagliyan, O., Karginov, A. V., Yagishita, S., Gale, M. E., Wang, H., Dermardirossian, C., Wells, C. M., Dokholyan, N. V., Kasai, H. & Hahn, K. M., Jul 21 2017, In : ACS Synthetic Biology. 6, 7, p. 1257-1262 6 p.

Research output: Contribution to journalArticle

p21-Activated Kinases
Sirolimus
Chemical activation
Switches
Graph theory
3 Citations

Ion-pulling simulations provide insights into the mechanisms of channel opening of the skeletal muscle ryanodine receptor

Mowrey, D. D., Xu, L., Mei, Y., Pasek, D. A., Meissner, G. & Dokholyan, N. V., Jan 1 2017, In : Journal of Biological Chemistry. 292, 31, p. 12947-12958 12 p.

Research output: Contribution to journalArticle

Ryanodine Receptor Calcium Release Channel
Muscle
Skeletal Muscle
Ions
Constriction

Molecular Mechanisms of the R61T Mutation in Apolipoprotein E4: A Dynamic Rescue

Williams, B., Convertino, M., Das, J. & Dokholyan, N. V., Nov 21 2017, In : Biophysical journal. 113, 10, p. 2192-2198 7 p.

Research output: Contribution to journalArticle

Apolipoprotein E4
Mutation
Alzheimer Disease
Apolipoprotein E2
Apolipoprotein E3
11 Citations

Physicochemical code for quinary protein interactions in Escherichia coli

Mu, X., Choi, S., Lang, L., Mowray, D., Dokholyan, N. V., Danielsson, J. & Oliveberg, M., Jun 6 2017, In : Proceedings of the National Academy of Sciences of the United States of America. 114, 23, p. E4556-E4563

Research output: Contribution to journalArticle

Escherichia coli
Proteins
Bacterial Proteins
Escherichia coli Proteins
Hydrophobic and Hydrophilic Interactions
7 Citations

Predicting the functional consequences of non-synonymous single nucleotide polymorphisms in IL8 gene

Dakal, T. C., Kala, D., Dhiman, G., Yadav, V., Krokhotin, A. & Dokholyan, N. V., Dec 1 2017, In : Scientific Reports. 7, 1, 6525.

Research output: Contribution to journalArticle

interleukin-8
single nucleotide polymorphism
stomach neoplasms
genes
amino acid substitution
2 Citations
Protein folding
protein folding
Protein Folding
folding
proteins
1 Citations

Redundant Functions for Nap1 and Chz1 in H2A.Z Deposition

Dronamraju, R., Ramachandran, S., Jha, D. K., Adams, A. T., Difiore, J. V., Parra, M. A., Dokholyan, N. V. & Strahl, B. D., Dec 1 2017, In : Scientific Reports. 7, 1, 10791.

Research output: Contribution to journalArticle

Heterochromatin
Histone Chaperones
Molecular Dynamics Simulation
Histones
DNA Damage
25 Citations

RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme

Miao, Z., Adamiak, R. W., Antczak, M., Batey, R. T., Becka, A. J., Biesiada, M., Boniecki, M. J., Bujnicki, J. M., Chen, S. J., Cheng, C. Y., Chou, F. C., Ferré-D'Amaré, A. R., Das, R., Dawson, W. K., Ding, F., Dokholyan, N. V., Dunin-Horkawicz, S., Geniesse, C., Kappel, K., Kladwang, W. & 26 othersKrokhotin, A., Łach, G. E., Major, F., Mann, T. H., Magnus, M., Pachulska-Wieczorek, K., Patel, D. J., Piccirilli, J. A., Popenda, M., Purzycka, K. J., Ren, A., Rice, G. M., Santalucia, J., Sarzynska, J., Szachniuk, M., Tandon, A., Trausch, J. J., Tian, S., Wang, J., Weeks, K. M., Williams, B., Xiao, Y., Xu, X., Zhang, D., Zok, T. & Westhof, E., May 1 2017, In : RNA. 23, 5, p. 655-672 18 p.

Research output: Contribution to journalArticle

Riboswitch
Catalytic RNA
RNA
Ligands
Glutamine
8 Citations

Solving protein structures using short-distance cross-linking constraints as a guide for discrete molecular dynamics simulations

Brodie, N. I., Popov, K. I., Petrotchenko, E. V., Dokholyan, N. V. & Borchers, C. H., Jul 5 2017, In : Science Advances. 3, 7, e1700479.

Research output: Contribution to journalArticle

Molecular dynamics
Computer simulation
Tacrolimus Binding Proteins
Protein folding
Proteins
1 Citations

Structure modeling of RNA using sparse NMR constraints

Williams, B., Zhao, B., Tandon, A., Ding, F., Weeks, K. M., Zhang, Q. & Dokholyan, N. V., Dec 15 2017, In : Nucleic acids research. 45, 22, p. 12638-12647 10 p.

Research output: Contribution to journalArticle

RNA
Molecular Dynamics Simulation
Molecular Conformation
Benchmarking
Nucleotide Motifs
5 Citations

Transmembrane helical interactions in the CFTR channel pore

Das, J., Aleksandrov, A. A., Cui, L., He, L., Riordan, J. R. & Dokholyan, N. V., Jun 1 2017, In : PLoS Computational Biology. 13, 6, e1005594.

Research output: Contribution to journalArticle

Fibrosis
Cystic Fibrosis Transmembrane Conductance Regulator
cystic fibrosis
Conductance
Regulator
2016

A hidden aggregation-prone structure in the heart of hypoxia inducible factor prolyl hydroxylase

Hadi-Alijanvand, H., Proctor, E. A., Ding, F., Dokholyan, N. V. & Moosavi-Movahedi, A. A., May 1 2016, In : Proteins: Structure, Function and Bioinformatics. 84, 5, p. 611-623 13 p.

Research output: Contribution to journalArticle

Prolyl Hydroxylases
Agglomeration
Protein Unfolding
Proteins
Molecular Dynamics Simulation
11 Citations

A modified PATH algorithm rapidly generates transition states comparable to those found by other well established algorithms

Chandrasekaran, S. N., Das, J., Dokholyan, N. V. & Carter, C. W., Jan 1 2016, In : Structural Dynamics. 3, 1, 012101.

Research output: Contribution to journalArticle

Proteins
Structural properties
Crystal structure
Trajectories
proteins
6 Citations

A Phosphomimetic Mutation Stabilizes SOD1 and Rescues Cell Viability in the Context of an ALS-Associated Mutation

Fay, J. M., Zhu, C., Proctor, E. A., Tao, Y., Cui, W., Ke, H. & Dokholyan, N. V., Nov 1 2016, In : Structure. 24, 11, p. 1898-1906 9 p.

Research output: Contribution to journalArticle

Amyotrophic Lateral Sclerosis
Cell Survival
Mutation
Poisons
Motor Neurons
16 Citations

Applications of Discrete Molecular Dynamics in biology and medicine

Proctor, E. A. & Dokholyan, N. V., Apr 1 2016, In : Current Opinion in Structural Biology. 37, p. 9-13 5 p.

Research output: Contribution to journalReview article

Molecular Dynamics Simulation
Medicine
Microcomputers
Proteostasis Deficiencies
Petroleum Pollution
1 Citations

Computational modeling of small molecule ligand binding interactions and affinities

Convertino, M. & Dokholyan, N. V., May 1 2016, Methods in Molecular Biology. Humana Press Inc., p. 23-32 10 p. (Methods in Molecular Biology; vol. 1414).

Research output: Chapter in Book/Report/Conference proceedingChapter

Ligands
Biological Phenomena
Preclinical Drug Evaluations
Proteins
Propranolol
29 Citations

Controlling Allosteric Networks in Proteins

Dokholyan, N. V., Jun 8 2016, In : Chemical Reviews. 116, 11, p. 6463-6487 25 p.

Research output: Contribution to journalReview article

Proteins
Ligands
Cystic Fibrosis Transmembrane Conductance Regulator
Biological systems
Binding Sites
7 Citations
Factor Xa
activity structure
Classifiers
Ligands
ranking
17 Citations

Dynamic Docking of Conformationally Constrained Macrocycles: Methods and Applications

Allen, S. E., Dokholyan, N. V. & Bowers, A. A., Jan 15 2016, In : ACS chemical biology. 11, 1, p. 10-24 15 p.

Research output: Contribution to journalReview article

Biological Products
Scaffolds
Pharmaceutical Chemistry
Point contacts
Proteins
33 Citations

Engineering extrinsic disorder to control protein activity in living cells

Dagliyan, O., Tarnawski, M., Chu, P. H., Shirvanyants, D., Schlichting, I., Dokholyan, N. V. & Hahn, K. M., Dec 16 2016, In : Science. 354, 6318, p. 1441-1444 4 p.

Research output: Contribution to journalArticle

Molecular Motor Proteins
Optogenetics
Proteins
Guanosine
Guanine
3 Citations

Gain-of-function mutation W493R in the epithelial sodium channel allosterically reconfigures intersubunit coupling

Shobair, M., Dagliyan, O., Kota, P., Dang, Y. L., He, H., Stutts, M. J. & Dokholyan, N. V., Feb 19 2016, In : Journal of Biological Chemistry. 291, 8, p. 3682-3692 11 p.

Research output: Contribution to journalArticle

Epithelial Sodium Channels
Molecular Dynamics Simulation
Water-Electrolyte Imbalance
Liddle Syndrome
Sodium
1 Citations

Harnessing Nature's Diversity: Discovering organophosphate bioscavenger characteristics among low molecular weight proteins

Jacob, R. B., Michaels, K. C., Anderson, C. J., Fay, J. M. & Dokholyan, N. V., Nov 15 2016, In : Scientific Reports. 6, 37175.

Research output: Contribution to journalArticle

Organophosphates
Organophosphate Poisoning
Molecular Weight
Acetylcholinesterase
Paraoxon
21 Citations

Nonnative SOD1 trimer is toxic to motor neurons in a model of amyotrophic lateral sclerosis

Proctor, E. A., Fee, L., Tao, Y., Redler, R. L., Fay, J. M., Zhang, Y., Lv, Z., Mercer, I. P., Deshmukh, M., Lyubchenko, Y. L. & Dokholyan, N. V., Jan 19 2016, In : Proceedings of the National Academy of Sciences of the United States of America. 113, 3, p. 614-619 6 p.

Research output: Contribution to journalArticle

Poisons
Amyotrophic Lateral Sclerosis
Motor Neurons
Mutation
Disease Progression
23 Citations

Pharmacological Chaperones: Design and Development of New Therapeutic Strategies for the Treatment of Conformational Diseases

Convertino, M., Das, J. & Dokholyan, N. V., Jun 17 2016, In : ACS chemical biology. 11, 6, p. 1471-1489 19 p.

Research output: Contribution to journalReview article

Pharmacology
Protein folding
Poisons
Protein Folding
Bioactivity
8 Citations

Protein Destabilization as a Common Factor in Diverse Inherited Disorders

Redler, R. L., Das, J., Diaz, J. R. & Dokholyan, N. V., Jan 1 2016, In : Journal of Molecular Evolution. 82, 1, p. 11-16 6 p.

Research output: Contribution to journalLetter

genetic disorders
protein
Amino Acid Substitution
Proteins
amino acid substitution
6 Citations

Restoration of R117H CFTR folding and function in human airway cells through combination treatment with VX-809 and VX-770

Gentzsch, M., Ren, H. Y., Houck, S. A., Quinney, N. L., Cholon, D. M., Sopha, P., Chaudhry, I. G., Das, J., Dokholyan, N. V., Randell, S. H. & Cyr, D. M., Jan 1 2016, In : American Journal of Physiology - Lung Cellular and Molecular Physiology. 311, 3, p. L550-L559

Research output: Contribution to journalArticle

Cystic Fibrosis
Mutation
Therapeutics
lumacaftor
ivacaftor
2015
10 Citations

ApoE4-specific Misfolded Intermediate Identified by Molecular Dynamics Simulations

Williams, B., Convertino, M., Das, J. & Dokholyan, N. V., Jan 1 2015, In : PLoS Computational Biology. 11, 10, e1004359.

Research output: Contribution to journalArticle

Apolipoprotein E4
protein isoforms
apolipoprotein E
Alzheimer's Disease
molecular dynamics
9 Citations

Channel gating dependence on pore lining helix glycine residues in skeletal muscle ryanodine receptor

Mei, Y., Xu, L., Mowrey, D. D., Giraldez, R. M., Wang, Y., Pasek, D. A., Dokholyan, N. V. & Meissner, G., Jul 10 2015, In : Journal of Biological Chemistry. 290, 28, p. 17535-17545 11 p.

Research output: Contribution to journalArticle

Ryanodine Receptor Calcium Release Channel
Linings
Glycine
Muscle
Skeletal Muscle
5 Citations

Computational methods toward accurate RNA structure prediction using coarse-grained and all-atom models

Krokhotin, A. & Dokholyan, N. V., Jan 1 2015, In : Methods in enzymology. 553, p. 65-89 25 p.

Research output: Contribution to journalReview article

Computational methods
RNA
Atoms
Nucleotides
Guide RNA
10 Citations

COMT gene locus: New functional variants

Meloto, C. B., Segall, S. K., Smith, S., Parisien, M., Shabalina, S. A., Rizzatti-Barbosa, C. M., Gauthier, J., Tsao, D., Convertino, M., Piltonen, M. H., Slade, G. D., Fillingim, R. B., Greenspan, J. D., Ohrbach, R., Knott, C., Maixner, W., Zaykin, D., Dokholyan, N. V., Reenila, I., Mannisto, P. T. & 1 othersDiatchenko, L., Oct 1 2015, In : Pain. 156, 10, p. 2072-2083 12 p.

Research output: Contribution to journalArticle

Catechol O-Methyltransferase
Genes
Pain
Protein Isoforms
Adrenergic Agents
8 Citations

Differences in the Antinociceptive Effects and Binding Properties of Propranolol and Bupranolol Enantiomers

Martin, L. J., Piltonen, M. H., Gauthier, J., Convertino, M., Acland, E. L., Dokholyan, N. V., Mogil, J. S., Diatchenko, L. & Maixner, W., Jan 1 2015, In : Journal of Pain. 16, 12, p. 1321-1333 13 p.

Research output: Contribution to journalArticle

Bupranolol
Propranolol
Adrenergic beta-Agonists
Receptors, Adrenergic, beta
Adrenergic Receptors
7 Citations

Differential regulation of 6- and 7-Transmembrane helix variants of μ-opioid receptor in response to morphine stimulation

Convertino, M., Samoshkin, A., Viet, C. T., Gauthier, J., Fraine, S. P. L., Sharif-Naeini, R., Schmidt, B. L., Maixner, W., Diatchenko, L. & Dokholyan, N. V., Nov 10 2015, In : PloS one. 10, 11, e0142826.

Research output: Contribution to journalArticle

morphine
mu Opioid Receptor
narcotics
Morphine
Opioid Analgesics
19 Citations

iFoldRNA v2: Folding RNA with constraints

Krokhotin, A., Houlihan, K. & Dokholyan, N. V., Feb 6 2015, In : Bioinformatics. 31, 17, p. 2891-2893 3 p.

Research output: Contribution to journalArticle

RNA Folding
Folding
RNA
Servers
Server
17 Citations

Light-cleavable rapamycin dimer as an optical trigger for protein dimerization

Brown, K. A., Zou, Y., Shirvanyants, D., Zhang, J., Samanta, S., Mantravadi, P. K., Dokholyan, N. V. & Deiters, A., Apr 4 2015, In : Chemical Communications. 51, 26, p. 5702-5705 4 p.

Research output: Contribution to journalArticle

Tacrolimus Binding Protein 1A
Dimerization
Sirolimus
Dimers
Proteins