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Items: 1 to 50 of 246

1.

Insight into the Structure of the "Unstructured" Tau Protein.

Popov KI, Makepeace KAT, Petrotchenko EV, Dokholyan NV, Borchers CH.

Structure. 2019 Oct 14. pii: S0969-2126(19)30309-0. doi: 10.1016/j.str.2019.09.003. [Epub ahead of print]

PMID:
31628033
2.

Distinct Binding Modes of Vinculin Isoforms Underlie Their Functional Differences.

Krokhotin A, Sarker M, Sevilla EA, Costantini LM, Griffith JD, Campbell SL, Dokholyan NV.

Structure. 2019 Oct 1;27(10):1527-1536.e3. doi: 10.1016/j.str.2019.07.013. Epub 2019 Aug 15.

PMID:
31422909
3.

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

Proctor EA, Mowrey DD, Dokholyan NV.

PLoS Comput Biol. 2019 Jul 19;15(7):e1007225. doi: 10.1371/journal.pcbi.1007225. eCollection 2019 Jul.

4.

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

Sapienza PJ, Popov KI, Mowrey DD, Falk BT, Dokholyan NV, Lee AL.

Biochemistry. 2019 Jul 30;58(30):3302-3313. doi: 10.1021/acs.biochem.9b00486. Epub 2019 Jul 18.

PMID:
31283187
5.

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

Rackley L, Stewart JM, Salotti J, Krokhotin A, Shah A, Halman JR, Juneja R, Smollett J, Lee L, Roark K, Viard M, Tarannum M, Vivero-Escoto J, Johnson PF, Dobrovolskaia MA, Dokholyan NV, Franco E, Afonin KA.

Adv Funct Mater. 2018 Nov 28;28(48). pii: 1805959. doi: 10.1002/adfm.201805959. Epub 2018 Oct 9.

PMID:
31258458
6.

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

Chirasani VR, Xu L, Addis HG, Pasek DA, Dokholyan NV, Meissner G, Yamaguchi N.

Am J Physiol Cell Physiol. 2019 Aug 1;317(2):C358-C365. doi: 10.1152/ajpcell.00052.2019. Epub 2019 Jun 5.

PMID:
31166712
7.

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

Zhu C, Han Q, Samoshkin A, Convertino M, Linton A, Faison EM, Ji RR, Diatchenko L, Dokholyan NV.

Proteins. 2019 Oct;87(10):878-884. doi: 10.1002/prot.25751. Epub 2019 Jun 12.

PMID:
31141214
8.

Molecular mechanisms of heterogeneous oligomerization of huntingtin proteins.

Bonfanti S, Lionetti MC, Fumagalli MR, Chirasani VR, Tiana G, Dokholyan NV, Zapperi S, La Porta CAM.

Sci Rep. 2019 May 20;9(1):7615. doi: 10.1038/s41598-019-44151-0.

9.

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

Wang J, Williams B, Chirasani VR, Krokhotin A, Das R, Dokholyan NV.

Nucleic Acids Res. 2019 Jun 20;47(11):5563-5572. doi: 10.1093/nar/gkz427.

10.

Engineering proteins for allosteric control by light or ligands.

Dagliyan O, Dokholyan NV, Hahn KM.

Nat Protoc. 2019 Jun;14(6):1863-1883. doi: 10.1038/s41596-019-0165-3. Epub 2019 May 10.

PMID:
31076662
11.

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

Reilley DJ, Popov KI, Dokholyan NV, Alexandrova AN.

J Phys Chem B. 2019 May 30;123(21):4534-4539. doi: 10.1021/acs.jpcb.9b02893. Epub 2019 May 17.

PMID:
31038957
12.

MedusaDock 2.0: Efficient and Accurate Protein-Ligand Docking With Constraints.

Wang J, Dokholyan NV.

J Chem Inf Model. 2019 Jun 24;59(6):2509-2515. doi: 10.1021/acs.jcim.8b00905. Epub 2019 Apr 17.

PMID:
30946779
13.

MERTK mediated novel site Akt phosphorylation alleviates SAV1 suppression.

Jiang Y, Zhang Y, Leung JY, Fan C, Popov KI, Su S, Qian J, Wang X, Holtzhausen A, Ubil E, Xiang Y, Davis I, Dokholyan NV, Wu G, Perou CM, Kim WY, Earp HS, Liu P.

Nat Commun. 2019 Apr 3;10(1):1515. doi: 10.1038/s41467-019-09233-7.

14.

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

Brodie NI, Popov KI, Petrotchenko EV, Dokholyan NV, Borchers CH.

PLoS Comput Biol. 2019 Mar 27;15(3):e1006859. doi: 10.1371/journal.pcbi.1006859. eCollection 2019 Mar.

15.

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 AS, Zhu C, Mo J, Zhang L, Tam JW, Ariel P, Zhao B, Zhang S, Ke H, Li P, Dokholyan NV, Duncan JA, Ting JP.

Immunity. 2019 Mar 19;50(3):591-599.e6. doi: 10.1016/j.immuni.2019.02.009.

16.

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

Sarker M, Lee HT, Mei L, Krokhotin A, de Los Reyes SE, Yen L, Costantini LM, Griffith J, Dokholyan NV, Alushin GM, Campbell SL.

J Mol Biol. 2019 Apr 5;431(8):1604-1618. doi: 10.1016/j.jmb.2019.02.024. Epub 2019 Mar 5.

17.

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

Zhu C, Dukhovlinova E, Council O, Ping L, Faison EM, Prabhu SS, Potter EL, Upton SL, Yin G, Fay JM, Kincer LP, Spielvogel E, Campbell SL, Benhabbour SR, Ke H, Swanstrom R, Dokholyan NV.

Nat Commun. 2019 Feb 27;10(1):948. doi: 10.1038/s41467-019-08876-w.

18.

Allostery in Its Many Disguises: From Theory to Applications.

Wodak SJ, Paci E, Dokholyan NV, Berezovsky IN, Horovitz A, Li J, Hilser VJ, Bahar I, Karanicolas J, Stock G, Hamm P, Stote RH, Eberhardt J, Chebaro Y, Dejaegere A, Cecchini M, Changeux JP, Bolhuis PG, Vreede J, Faccioli P, Orioli S, Ravasio R, Yan L, Brito C, Wyart M, Gkeka P, Rivalta I, Palermo G, McCammon JA, Panecka-Hofman J, Wade RC, Di Pizio A, Niv MY, Nussinov R, Tsai CJ, Jang H, Padhorny D, Kozakov D, McLeish T.

Structure. 2019 Apr 2;27(4):566-578. doi: 10.1016/j.str.2019.01.003. Epub 2019 Feb 7. Review.

19.

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 RF, Rangel MC, Wang J, Viard M, Richardson M, Khisamutdinov EF, Panigaj M, Dokholyan NV, Chammas R, Dobrovolskaia MA, Afonin KA.

Nucleic Acids Res. 2019 Feb 20;47(3):1350-1361. doi: 10.1093/nar/gky1215.

20.

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

Xu L, Chirasani VR, Carter JS, Pasek DA, Dokholyan NV, Yamaguchi N, Meissner G.

J Biol Chem. 2018 Dec 14;293(50):19501-19509. doi: 10.1074/jbc.RA118.004453. Epub 2018 Oct 19.

PMID:
30341173
21.

Computational design of chemogenetic and optogenetic split proteins.

Dagliyan O, Krokhotin A, Ozkan-Dagliyan I, Deiters A, Der CJ, Hahn KM, Dokholyan NV.

Nat Commun. 2018 Oct 2;9(1):4042. doi: 10.1038/s41467-018-06531-4.

22.

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

Luo J, Samanta S, Convertino M, Dokholyan NV, Deiters A.

Chembiochem. 2018 Oct 18;19(20):2178-2185. doi: 10.1002/cbic.201800226. Epub 2018 Oct 2.

23.

p62-Dependent Phase Separation of Patient-Derived KEAP1 Mutations and NRF2.

Cloer EW, Siesser PF, Cousins EM, Goldfarb D, Mowrey DD, Harrison JS, Weir SJ, Dokholyan NV, Major MB.

Mol Cell Biol. 2018 Oct 29;38(22). pii: e00644-17. doi: 10.1128/MCB.00644-17. Print 2018 Nov 15.

24.

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

Han Q, Liu D, Convertino M, Wang Z, Jiang C, Kim YH, Luo X, Zhang X, Nackley A, Dokholyan NV, Ji RR.

Neuron. 2018 Aug 8;99(3):449-463.e6. doi: 10.1016/j.neuron.2018.06.039. Epub 2018 Jul 19.

25.

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

Wang C, Aleksandrov AA, Yang Z, Forouhar F, Proctor EA, Kota P, An J, Kaplan A, Khazanov N, Boël G, Stockwell BR, Senderowitz H, Dokholyan NV, Riordan JR, Brouillette CG, Hunt JF.

J Biol Chem. 2018 Nov 16;293(46):17685-17704. doi: 10.1074/jbc.RA117.000819. Epub 2018 Jun 14.

PMID:
29903914
26.

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

Zhu C, Beck MV, Griffith JD, Deshmukh M, Dokholyan NV.

Proc Natl Acad Sci U S A. 2018 May 1;115(18):4661-4665. doi: 10.1073/pnas.1800187115. Epub 2018 Apr 16.

27.

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

Zhang Y, Hashemi M, Lv Z, Williams B, Popov KI, Dokholyan NV, Lyubchenko YL.

J Chem Phys. 2018 Mar 28;148(12):123322. doi: 10.1063/1.5008874.

28.

Tyrosine phosphorylation switching of a G protein.

Li B, Tunc-Ozdemir M, Urano D, Jia H, Werth EG, Mowrey DD, Hicks LM, Dokholyan NV, Torres MP, Jones AM.

J Biol Chem. 2018 Mar 30;293(13):4752-4766. doi: 10.1074/jbc.RA117.000163. Epub 2018 Jan 30.

29.

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

Shobair M, Popov KI, Dang YL, He H, Stutts MJ, Dokholyan NV.

J Biol Chem. 2018 Mar 9;293(10):3675-3684. doi: 10.1074/jbc.RA117.000604. Epub 2018 Jan 22.

30.

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

Xu L, Mowrey DD, Chirasani VR, Wang Y, Pasek DA, Dokholyan NV, Meissner G.

J Biol Chem. 2018 Feb 9;293(6):2015-2028. doi: 10.1074/jbc.M117.803247. Epub 2017 Dec 18.

31.

Structure modeling of RNA using sparse NMR constraints.

Williams B 2nd, Zhao B, Tandon A, Ding F, Weeks KM, Zhang Q, Dokholyan NV.

Nucleic Acids Res. 2017 Dec 15;45(22):12638-12647. doi: 10.1093/nar/gkx1058.

32.

Structural complexity and functional diversity of plant NADPH oxidases.

Kaur G, Guruprasad K, Temple BRS, Shirvanyants DG, Dokholyan NV, Pati PK.

Amino Acids. 2018 Jan;50(1):79-94. doi: 10.1007/s00726-017-2491-5. Epub 2017 Oct 25.

33.

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

Williams B 2nd, Convertino M, Das J, Dokholyan NV.

Biophys J. 2017 Nov 21;113(10):2192-2198. doi: 10.1016/j.bpj.2017.08.026. Epub 2017 Sep 12.

34.

Redundant Functions for Nap1 and Chz1 in H2A.Z Deposition.

Dronamraju R, Ramachandran S, Jha DK, Adams AT, DiFiore JV, Parra MA, Dokholyan NV, Strahl BD.

Sci Rep. 2017 Sep 7;7(1):10791. doi: 10.1038/s41598-017-11003-8.

35.

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

Dakal TC, Kala D, Dhiman G, Yadav V, Krokhotin A, Dokholyan NV.

Sci Rep. 2017 Jul 26;7(1):6525. doi: 10.1038/s41598-017-06575-4.

36.

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

Brodie NI, Popov KI, Petrotchenko EV, Dokholyan NV, Borchers CH.

Sci Adv. 2017 Jul 7;3(7):e1700479. doi: 10.1126/sciadv.1700479. eCollection 2017 Jul.

37.

Transmembrane helical interactions in the CFTR channel pore.

Das J, Aleksandrov AA, Cui L, He L, Riordan JR, Dokholyan NV.

PLoS Comput Biol. 2017 Jun 22;13(6):e1005594. doi: 10.1371/journal.pcbi.1005594. eCollection 2017 Jun.

38.

Comparative Visualization of the RNA Suboptimal Conformational Ensemble In Vivo.

Woods CT, Lackey L, Williams B, Dokholyan NV, Gotz D, Laederach A.

Biophys J. 2017 Jul 25;113(2):290-301. doi: 10.1016/j.bpj.2017.05.031. Epub 2017 Jun 15.

39.

Protein folding: Over half a century lasting quest: Comment on "There and back again: Two views on the protein folding puzzle" by Alexei V. Finkelstein et al.

Krokhotin A, Dokholyan NV.

Phys Life Rev. 2017 Jul;21:72-74. doi: 10.1016/j.plrev.2017.06.002. Epub 2017 Jun 14. No abstract available.

PMID:
28599786
40.

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

Mowrey DD, Xu L, Mei Y, Pasek DA, Meissner G, Dokholyan NV.

J Biol Chem. 2017 Aug 4;292(31):12947-12958. doi: 10.1074/jbc.M116.760199. Epub 2017 Jun 5.

41.

Physicochemical code for quinary protein interactions in Escherichia coli.

Mu X, Choi S, Lang L, Mowray D, Dokholyan NV, Danielsson J, Oliveberg M.

Proc Natl Acad Sci U S A. 2017 Jun 6;114(23):E4556-E4563. doi: 10.1073/pnas.1621227114. Epub 2017 May 23.

42.

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

Jacob RB, Michaels KC, Anderson CJ, Fay JM, Dokholyan NV.

Sci Rep. 2017 Apr 28;7:46727. doi: 10.1038/srep46727. No abstract available.

43.

Engineering Pak1 Allosteric Switches.

Dagliyan O, Karginov AV, Yagishita S, Gale ME, Wang H, DerMardirossian C, Wells CM, Dokholyan NV, Kasai H, Hahn KM.

ACS Synth Biol. 2017 Jul 21;6(7):1257-1262. doi: 10.1021/acssynbio.6b00359. Epub 2017 Apr 6.

44.

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

Jacob RB, Michaels KC, Anderson CJ, Fay JM, Dokholyan NV.

Sci Rep. 2017 Feb 17;7:42832. doi: 10.1038/srep42832. No abstract available.

45.

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

Miao Z, Adamiak RW, Antczak M, Batey RT, Becka AJ, Biesiada M, Boniecki MJ, Bujnicki JM, Chen SJ, Cheng CY, Chou FC, Ferré-D'Amaré AR, Das R, Dawson WK, Ding F, Dokholyan NV, Dunin-Horkawicz S, Geniesse C, Kappel K, Kladwang W, Krokhotin A, Łach GE, Major F, Mann TH, Magnus M, Pachulska-Wieczorek K, Patel DJ, Piccirilli JA, Popenda M, Purzycka KJ, Ren A, Rice GM, Santalucia J Jr, Sarzynska J, Szachniuk M, Tandon A, Trausch JJ, Tian S, Wang J, Weeks KM, Williams B 2nd, Xiao Y, Xu X, Zhang D, Zok T, Westhof E.

RNA. 2017 May;23(5):655-672. doi: 10.1261/rna.060368.116. Epub 2017 Jan 30.

46.

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

Thompson PM, Ramachandran S, Case LB, Tolbert CE, Tandon A, Pershad M, Dokholyan NV, Waterman CM, Campbell SL.

Structure. 2017 Feb 7;25(2):264-275. doi: 10.1016/j.str.2016.12.002. Epub 2017 Jan 12.

47.

Engineering extrinsic disorder to control protein activity in living cells.

Dagliyan O, Tarnawski M, Chu PH, Shirvanyants D, Schlichting I, Dokholyan NV, Hahn KM.

Science. 2016 Dec 16;354(6318):1441-1444.

48.

Computational Protein Design Through Grafting and Stabilization.

Zhu C, Mowrey DD, Dokholyan NV.

Methods Mol Biol. 2017;1529:227-241.

PMID:
27914054
49.

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

Jacob RB, Michaels KC, Anderson CJ, Fay JM, Dokholyan NV.

Sci Rep. 2016 Nov 15;6:37175. doi: 10.1038/srep37175. Erratum in: Sci Rep. 2017 Feb 17;7:42832. Sci Rep. 2017 Apr 28;7:46727.

50.

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

Krokhotin A, Mustoe AM, Weeks KM, Dokholyan NV.

RNA. 2017 Jan;23(1):6-13. Epub 2016 Nov 1.

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