Works matching AU Lyumkis, Dmitry

Results: 18

Multivalent interactions essential for lentiviral integrase function.

Published in:

Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-29928-8

By:

Ballandras-Colas, Allison;
Chivukula, Vidya;
Gruszka, Dominika T.;
Shan, Zelin;
Singh, Parmit K.;
Pye, Valerie E.;
McLean, Rebecca K.;
Bedwell, Gregory J.;
Li, Wen;
Nans, Andrea;
Cook, Nicola J.;
Fadel, Hind J.;
Poeschla, Eric M.;
Griffiths, David J.;
Vargas, Javier;
Taylor, Ian A.;
Lyumkis, Dmitry;
Yardimci, Hasan;
Engelman, Alan N.;
Cherepanov, Peter

Publication type:

Article

Mechanism of Activation of SgrAI via Enzyme Filamentation and Mechanism of DNA Sequence Specificity Expansion.

Published in:

FASEB Journal, 2022, v. 36, p. N.PAG, doi. 10.1096/fasebj.2022.36.S1.0R839

By:

Horton, Nancy;
Ghadirian, Niloofar;
Shan, Zelin;
Lyumkis, Dmitry

Publication type:

Article

Structures, Mechanism, and Functional Relevance of Filament Formation by SgrAI.

Published in:

FASEB Journal, 2022, v. 36, p. N.PAG, doi. 10.1096/fasebj.2022.36.S1.L7804

By:

Ghadirian, Niloofar;
Shan, Zelin;
Lyumkis, Dmitry;
Horton, Nancy

Publication type:

Article

Sub-2 Å Ewald curvature corrected structure of an AAV2 capsid variant.

Published in:

Nature Communications, 2018, v. 9, n. 1, p. 1, doi. 10.1038/s41467-018-06076-6

By:

Tan, Yong Zi;
Aiyer, Sriram;
Mietzsch, Mario;
Hull, Joshua A.;
McKenna, Robert;
Grieger, Joshua;
Samulski, R. Jude;
Baker, Timothy S.;
Agbandje-McKenna, Mavis;
Lyumkis, Dmitry

Publication type:

Article

CryoFAST™: Automated Cryo-Electron Microscopy Data Acquisition Using Machine Learning.

Published in:

2023

By:

Kumar, Narasimha;
Gray, Elliot;
Lyumkis, Dmitry;
Mehrani, Atousa

Publication type:

Abstract

Anisotropy in CryoEM Resolution is Dominated by Preferred Orientations, but not Structure Factors: A Study Using a Highly Symmetric Structure.

Published in:

2023

By:

Baldwin, Philip R;
Aiyer, Sriram;
Strutzenberg, Timothy S;
Lyumkis, Dmitry

Publication type:

Abstract

Automation of Angular Reconstitution for Facilitating the Construction of Initial Models in Single-Particle Electron Microscopy.

Published in:

2010

By:

Lyumkis, Dmitry;
Nayak, Sunita;
Milligan, Ronald R.;
Potter, Clinton S.;
Carragher, Bridget

Publication type:

Abstract

Molecular determinants for dsDNA translocation by the transcription-repair coupling and evolvability factor Mfd.

Published in:

Nature Communications, 2020, v. 11, n. 1, p. 1, doi. 10.1038/s41467-020-17457-1

By:

Brugger, Christiane;
Zhang, Cheng;
Suhanovsky, Margaret M.;
Kim, David D.;
Sinclair, Amy N.;
Lyumkis, Dmitry;
Deaconescu, Alexandra M.

Publication type:

Article

Structures, mechanisms, and kinetic advantages of the SgrAI filament forming mechanism.

Published in:

Critical Reviews in Biochemistry & Molecular Biology, 2024, v. 59, n. 6, p. 363, doi. 10.1080/10409238.2024.2440315

By:

Horton, Nancy C.;
Lyumkis, Dmitry

Publication type:

Article

Assembly of the bacterial ribosome with circularly permuted rRNA.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 18, p. 11254, doi. 10.1093/nar/gkae636

By:

Dong, Xiyu;
Sheng, Kai;
Gebert, Luca F R;
Aiyer, Sriram;
MacRae, Ian J;
Lyumkis, Dmitry;
Williamson, James R

Publication type:

Article

Near-physiological in vitro assembly of 50S ribosomes involves parallel pathways.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 6, p. 2862, doi. 10.1093/nar/gkad082

By:

Dong, Xiyu;
Doerfel, Lili K;
Sheng, Kai;
Rabuck-Gibbons, Jessica N;
Popova, Anna M;
Lyumkis, Dmitry;
Williamson, James R

Publication type:

Article

B-to-A transition in target DNA during retroviral integration.

Published in:

Nucleic Acids Research, 2022, v. 50, n. 15, p. 8898, doi. 10.1093/nar/gkac644

By:

Jóźwik, Ilona K;
Li, Wen;
Zhang, Da-Wei;
Wong, Doris;
Grawenhoff, Julia;
Ballandras-Colas, Allison;
Aiyer, Sriram;
Cherepanov, Peter;
Engelman, Alan N;
Lyumkis, Dmitry

Publication type:

Article

Elucidating the Molecular Determinants of the Binding Modes of a Third-Generation HIV-1 Integrase Strand Transfer Inhibitor: The Importance of Side Chain and Solvent Reorganization.

Published in:

Viruses (1999-4915), 2024, v. 16, n. 1, p. 76, doi. 10.3390/v16010076

By:

Sun, Qinfang;
Biswas, Avik;
Lyumkis, Dmitry;
Levy, Ronald;
Deng, Nanjie

Publication type:

Article

Integrase Strand Transfer Inhibitors Are Effective Anti-HIV Drugs.

Published in:

Viruses (1999-4915), 2021, v. 13, n. 2, p. 205, doi. 10.3390/v13020205

By:

Smith, Steven J.;
Zhao, Xue Zhi;
Passos, Dario Oliveira;
Lyumkis, Dmitry;
Burke Jr., Terrence R.;
Hughes, Stephen H.;
Grandgenett, Duane P.;
Zoulim, Fabien

Publication type:

Article

Missing Wedge Completion via Unsupervised Learning with Coordinate Networks.

Published in:

International Journal of Molecular Sciences, 2024, v. 25, n. 10, p. 5473, doi. 10.3390/ijms25105473

By:

Van Veen, Dave;
Galaz-Montoya, Jesús G.;
Shen, Liyue;
Baldwin, Philip;
Chaudhari, Akshay S.;
Lyumkis, Dmitry;
Schmid, Michael F.;
Chiu, Wah;
Pauly, John

Publication type:

Article

A unified Watson-Crick geometry drives transcription of six-letter expanded DNA alphabets by E. coli RNA polymerase.

Published in:

Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-023-43735-9

By:

Oh, Juntaek;
Shan, Zelin;
Hoshika, Shuichi;
Xu, Jun;
Chong, Jenny;
Benner, Steven A.;
Lyumkis, Dmitry;
Wang, Dong

Publication type:

Article

Assembly landscape for the bacterial large ribosomal subunit.

Published in:

Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-023-40859-w

By:

Sheng, Kai;
Li, Ning;
Rabuck-Gibbons, Jessica N.;
Dong, Xiyu;
Lyumkis, Dmitry;
Williamson, James R.

Publication type:

Article

The role of filamentation in activation and DNA sequence specificity of the sequence-specific endonuclease SgrAI.

Published in:

Biochemical Society Transactions, 2022, v. 50, n. 6, p. 1703, doi. 10.1042/BST20220547

By:

Lyumkis, Dmitry;
Horton, Nancy C.

Publication type:

Article