• 11322 Citations
  • 59 h-Index
1994 …2020

Research output per year

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Research Output

2020

Alternative Splicing of Opioid Receptor Genes Shows a Conserved Pattern for 6TM Receptor Variants

Piltonen, M., Krokhotin, A., Parisien, M., Bérubé, P., Djambazian, H., Sladek, R., Dokholyan, N. V., Shabalina, S. A. & Diatchenko, L., 2020, (Accepted/In press) In : Cellular and Molecular Neurobiology.

Research output: Contribution to journalArticle

Development of a Novel Multi-Isoform ALDH Inhibitor Effective as an Antimelanoma Agent

Dinavahi, S. S., Gowda, R., Gowda, K., Bazewicz, C. G., Chirasani, V. R., Battu, M. B., Berg, A., Dokholyan, N. V., Amin, S. & Robertson, G. P., Feb 1 2020, In : Molecular cancer therapeutics. 19, 2, p. 447-459 13 p.

Research output: Contribution to journalArticle

1 Scopus citations

Experimentally-driven protein structure modeling

Dokholyan, N. V., May 30 2020, In : Journal of Proteomics. 220, 103777.

Research output: Contribution to journalReview article

1 Scopus citations

Ligand-induced disorder-to-order transitions characterized by structural proteomics and molecular dynamics simulations

Makepeace, K. A. T., Brodie, N. I., Popov, K. I., Gudavicius, G., Nelson, C. J., Petrotchenko, E. V., Dokholyan, N. V. & Borchers, C. H., Jan 16 2020, In : Journal of Proteomics. 211, 103544.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Single-channel properties of skeletal muscle ryanodine receptor pore Δ4923FF4924 in two brothers with a lethal form of fetal akinesia

Xu, L., Harms, F. L., Chirasani, V. R., Pasek, D. A., Kortüm, F., Meinecke, P., Dokholyan, N. V., Kutsche, K. & Meissner, G., May 2020, In : Cell Calcium. 87, 102182.

Research output: Contribution to journalArticle

1 Scopus citations
2019

A central core disease mutation in the Ca2+-binding site of skeletal muscle ryanodine receptor impairs single-channel regulation

Chirasani, V. R., Xu, L., Addis, H. G., Pasek, D. A., Dokholyan, N. V., Meissner, G. & Yamaguchi, N., Aug 2019, In : American Journal of Physiology - Cell Physiology. 317, 2, p. C358-C365

Research output: Contribution to journalArticle

3 Scopus citations

Allostery in Its Many Disguises: From Theory to Applications

Wodak, S. J., Paci, E., Dokholyan, N. V., Berezovsky, I. N., Horovitz, A., Li, J., Hilser, V. J., Bahar, I., Karanicolas, J., Stock, G., Hamm, P., Stote, R. H., Eberhardt, J., Chebaro, Y., Dejaegere, A., Cecchini, M., Changeux, J. P., Bolhuis, P. G., Vreede, J., Faccioli, P. & 19 others, Orioli, S., Ravasio, R., Yan, L., Brito, C., Wyart, M., Gkeka, P., Rivalta, I., Palermo, G., McCammon, J. A., Panecka-Hofman, J., Wade, R. C., Di Pizio, A., Niv, M. Y., Nussinov, R., Tsai, C. J., Jang, H., Padhorny, D., Kozakov, D. & McLeish, T., Apr 2 2019, In : Structure. 27, 4, p. 566-578 13 p.

Research output: Contribution to journalReview article

45 Scopus citations

Cardiomyopathy Mutations in Metavinculin Disrupt Regulation of Vinculin-Induced F-Actin Assemblies

Sarker, M., Lee, H. T., Mei, L., Krokhotin, A., de los Reyes, S. E., Yen, L., Costantini, L. M., Griffith, J., Dokholyan, N. V., Alushin, G. M. & Campbell, S. L., Apr 5 2019, In : Journal of Molecular Biology. 431, 8, p. 1604-1618 15 p.

Research output: Contribution to journalArticle

1 Scopus citations

Computationally Guided Design of Single-Chain Variable Fragment Improves Specificity of Chimeric Antigen Receptors

Krokhotin, A., Du, H., Hirabayashi, K., Popov, K., Kurokawa, T., Wan, X., Ferrone, S., Dotti, G. & Dokholyan, N. V., Dec 20 2019, In : Molecular Therapy - Oncolytics. 15, p. 30-37 8 p.

Research output: Contribution to journalArticle

Open Access
2 Scopus citations

Conformational ensemble of native α-synuclein in solution as determined by short-distance crosslinking constraint-guided discrete molecular dynamics simulations

Brodie, N. I., Popov, K. I., Petrotchenko, E. V., Dokholyan, N. V. & Borchers, C. H., Mar 2019, In : PLoS computational biology. 15, 3, e1006859.

Research output: Contribution to journalArticle

Open Access
9 Scopus citations

Distinct Binding Modes of Vinculin Isoforms Underlie Their Functional Differences

Krokhotin, A., Sarker, M., Sevilla, E. A., Costantini, L. M., Griffith, J. D., Campbell, S. L. & Dokholyan, N. V., Oct 1 2019, In : Structure. 27, 10, p. 1527-1536.e3

Research output: Contribution to journalArticle

Engineering proteins for allosteric control by light or ligands

Dagliyan, O., Dokholyan, N. V. & Hahn, K. M., Jun 1 2019, In : Nature Protocols. 14, 6, p. 1863-1883 21 p.

Research output: Contribution to journalArticle

8 Scopus citations

Insight into the Structure of the “Unstructured” Tau Protein

Popov, K. I., Makepeace, K. A. T., Petrotchenko, E. V., Dokholyan, N. V. & Borchers, C. H., Nov 5 2019, In : Structure. 27, 11, p. 1710-1715.e4

Research output: Contribution to journalArticle

6 Scopus citations

Inter-Active Site Communication Mediated by the Dimer Interface β-Sheet in the Half-the-Sites Enzyme, Thymidylate Synthase

Sapienza, P. J., Popov, K. I., Mowrey, D. D., Falk, B. T., Dokholyan, N. & Lee, A. L., Jul 30 2019, In : Biochemistry. 58, 30, p. 3302-3313 12 p.

Research output: Contribution to journalArticle

Limits in accuracy and a strategy of RNA structure prediction using experimental information

Wang, J., Williams, B., Chirasani, V. R., Krokhotin, A., Das, R. & Dokholyan, N. V., 2019, In : Nucleic acids research. 47, 11, p. 5563-5572 10 p.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

MedusaDock 2.0: Efficient and Accurate Protein-Ligand Docking with Constraints

Wang, J. & Dokholyan, N., Jun 24 2019, In : Journal of Chemical Information and Modeling. 59, 6, p. 2509-2515 7 p.

Research output: Contribution to journalArticle

2 Scopus citations

MERTK mediated novel site Akt phosphorylation alleviates SAV1 suppression

Jiang, Y., Zhang, Y., Leung, J. Y., Fan, C., Popov, K. I., Su, S., Qian, J., Wang, X., Holtzhausen, A., Ubil, E., Xiang, Y., Davis, I., Dokholyan, N. V., Wu, G., Perou, C. M., Kim, W. Y., Earp, H. S. & Liu, P., Dec 1 2019, In : Nature communications. 10, 1, 1515.

Research output: Contribution to journalArticle

Open Access
5 Scopus citations

Molecular mechanisms of heterogeneous oligomerization of huntingtin proteins

Bonfanti, S., Lionetti, M. C., Fumagalli, M. R., Chirasani, V. R., Tiana, G., Dokholyan, N. V., Zapperi, S. & La Porta, C. A. M., Dec 1 2019, In : Scientific reports. 9, 1, 7615.

Research output: Contribution to journalArticle

Open Access
4 Scopus citations

Rationally designed carbohydrate-occluded epitopes elicit HIV-1 Env-specific antibodies

Zhu, C., Dukhovlinova, E., Council, O., Ping, L., Faison, E. M., Prabhu, S. S., Potter, E. L., Upton, S. L., Yin, G., Fay, J. M., Kincer, L. P., Spielvogel, E., Campbell, S. L., Benhabbour, S. R., Ke, H., Swanstrom, R. & Dokholyan, N. V., Dec 1 2019, In : Nature communications. 10, 1, 948.

Research output: Contribution to journalArticle

3 Scopus citations

RNA-DNA fibers and polygons with controlled immunorecognition activate RNAi, FRET and transcriptional regulation of NF-κB in human cells

Ke, W., Hong, E., Saito, R. F., Rangel, M. C., Wang, J., Viard, M., Richardson, M., Khisamutdinov, E. F., Panigaj, M., Dokholyan, N. V., Chammas, R., Dobrovolskaia, M. A. & Afonin, K. A., 2019, In : Nucleic acids research. 47, 3, p. 1350-1361 12 p.

Research output: Contribution to journalArticle

Open Access
15 Scopus citations

Stabilization of μ-opioid receptor facilitates its cellular translocation and signaling

Zhu, C., Han, Q., Samoshkin, A., Convertino, M., Linton, A., Faison, E. M., Ji, R. R., Diatchenko, L. & Dokholyan, N. V., Oct 1 2019, In : Proteins: Structure, Function and Bioinformatics. 87, 10, p. 878-884 7 p.

Research output: Contribution to journalArticle

2 Scopus citations

Uncovered Dynamic Coupling Resolves the Ambiguous Mechanism of Phenylalanine Hydroxylase Oxygen Binding

Reilley, D. J., Popov, K. I., Dokholyan, N. V. & Alexandrova, A. N., May 30 2019, In : Journal of Physical Chemistry B. 123, 21, p. 4534-4539 6 p.

Research output: Contribution to journalArticle

3 Scopus citations

Viral DNA Binding to NLRC3, an Inhibitory Nucleic Acid Sensor, Unleashes STING, a Cyclic Dinucleotide Receptor that Activates Type I Interferon

Li, X., Deng, M., Petrucelli, A. S., Zhu, C., Mo, J., Zhang, L., Tam, J. W., Ariel, P., Zhao, B., Zhang, S., Ke, H., Li, P., Dokholyan, N. V., Duncan, J. A. & Ting, J. P. Y., Mar 19 2019, In : Immunity. 50, 3, p. 591-599.e6

Research output: Contribution to journalArticle

13 Scopus citations

β-Methylamino-L-alanine substitution of serine in SOD1 suggests a direct role in ALS etiology

Proctor, E. A., Mowrey, D. D. & Dokholyan, N. V., Jul 2019, In : PLoS computational biology. 15, 7, e1007225.

Research output: Contribution to journalArticle

Open Access
3 Scopus citations
2018

Ca2-mediated activation of the skeletal-muscle ryanodine receptor ion channel

Xu, L., Chirasani, V. R., Carter, J. S., Pasek, D. A., Dokholyan, N. V., Yamaguchi, N. & Meissner, G., Dec 14 2018, In : Journal of Biological Chemistry. 293, 50, p. 19501-19509 9 p.

Research output: Contribution to journalArticle

6 Scopus citations

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

16 Scopus citations

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., Feb 9 2018, In : Journal of Biological Chemistry. 293, 6, p. 2015-2028 14 p.

Research output: Contribution to journalArticle

6 Scopus 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

21 Scopus citations

Large SOD1 aggregates, unlike trimeric SOD1, do not impact cell viability in a model of amyotrophic lateral sclerosis

Zhu, C., Beck, M. V., Griffith, J. D., Deshmukh, M. & Dokholyan, N. V., May 1 2018, In : Proceedings of the National Academy of Sciences of the United States of America. 115, 18, p. 4661-4665 5 p.

Research output: Contribution to journalArticle

15 Scopus citations

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., Nov 16 2018, In : Journal of Biological Chemistry. 293, 46, p. 17685-17704 20 p.

Research output: Contribution to journalArticle

3 Scopus citations

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., Mar 9 2018, In : Journal of Biological Chemistry. 293, 10, p. 3675-3684 10 p.

Research output: Contribution to journalArticle

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., Nackley, A., Dokholyan, N. V. & Ji, R. R., Aug 8 2018, In : Neuron. 99, 3, p. 449-463.e6

Research output: Contribution to journalArticle

20 Scopus citations

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

13 Scopus citations

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

12 Scopus citations

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., Nov 28 2018, In : Advanced Functional Materials. 28, 48, 1805959.

Research output: Contribution to journalArticle

18 Scopus citations

Structural complexity and functional diversity of plant NADPH oxidases

Kaur, G., Guruprasad, K., Temple, B. R. S., 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

9 Scopus 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., Mar 30 2018, In : Journal of Biological Chemistry. 293, 13, p. 4752-4766 15 p.

Research output: Contribution to journalArticle

9 Scopus citations
2017

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

8 Scopus 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

14 Scopus citations

Computational protein design through grafting and stabilization

Zhu, C., Mowrey, D. D. & Dokholyan, N., 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

5 Scopus citations

Corrigendum: 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., Feb 17 2017, In : Scientific reports. 7, p. 42832 1 p.

Research output: Contribution to journalComment/debate

Open Access

Corrigendum: 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., Apr 28 2017, In : Scientific reports. 7, p. 46727 1 p., 46727.

Research output: Contribution to journalComment/debate

Open Access
1 Scopus citations

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

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

Research output: Contribution to journalArticle

11 Scopus 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

10 Scopus 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., Aug 4 2017, In : Journal of Biological Chemistry. 292, 31, p. 12947-12958 12 p.

Research output: Contribution to journalArticle

6 Scopus citations

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

1 Scopus 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

48 Scopus 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., Dec 1 2017, In : Scientific reports. 7, 1, 6525.

Research output: Contribution to journalArticle

26 Scopus 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

4 Scopus citations