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Dmitry Lyumkis
Salk Institute for Biological Studies
51Publications
18H-index
2,638Citations
Publications 54
Newest
#1Philip R Baldwin (Salk Institute for Biological Studies)H-Index: 3
#2Dmitry Lyumkis (Salk Institute for Biological Studies)H-Index: 18
Abstract Virtually all single-particle cryo-EM experiments currently suffer from specimen adherence to the air-water interface, leading to a non-uniform distribution in the set of projection views. Whereas it is well accepted that uniform projection distributions can lead to high-resolution reconstructions, non-uniform (anisotropic) distributions can negatively affect map quality, elongate structural features, and in some cases, prohibit interpretation altogether. Although some consequences of n...
2 CitationsSource
#1Jessica N. Rabuck-Gibbons (Scripps Research Institute)
#2Anna Popova (Scripps Research Institute)
Last.James R. Williamson (Scripps Research Institute)H-Index: 58
view all 6 authors...
Abstract RNA helicases play various roles in ribosome biogenesis depending on the ribosome assembly pathway and stress state of the cell. However, it is unclear how most RNA helicases interact with ribosome assembly intermediates or on other cell processes to regulate ribosome assembly. SrmB is a DEAD-box helicase that acts early in the ribosome assembly process, although very little is known about its mechanism of action. Here, we use a combined quantitative mass spectrometry/cryo-electron micr...
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#1Smarajit Polley (Bose Institute)H-Index: 6
#2Dmitry Lyumkis (Salk Institute for Biological Studies)H-Index: 18
Last.Nancy C. Horton (UA: University of Arizona)H-Index: 19
view all 3 authors...
Summary Filament formation by enzymes is increasingly recognized as an important phenomenon with potentially unique regulatory properties and biological roles. SgrAI is an allosterically regulated type II restriction endonuclease that forms filaments with enhanced DNA cleavage activity and altered sequence specificity. Here, we present the cryoelectron microscopy (cryo-EM) structure of the filament of SgrAI in its activated configuration. The structural data illuminate the mechanistic origin of ...
2 CitationsSource
#2Xiaodong YanH-Index: 10
Last.Navtej ToorH-Index: 12
view all 7 authors...
Source
#2Xiaodong YanH-Index: 10
Last.Navtej ToorH-Index: 12
view all 7 authors...
Source
#1Cheng Zhang (Salk Institute for Biological Studies)H-Index: 2
#2William A. Cantara (OSU: Ohio State University)H-Index: 7
Last.Dmitry Lyumkis (Salk Institute for Biological Studies)H-Index: 18
view all 6 authors...
Abstract Single-particle electron cryo-microscopy and computational image classification can be used to analyze structural variability in macromolecules and their assemblies. In some cases, a particle may contain different regions that each display a range of distinct conformations. We have developed strategies, implemented within the Frealign and cisTEM image processing packages, to focus-classify on specific regions of a particle and detect potential covariance. The strategies are based on mas...
6 CitationsSource
#1Daniel B. Haack (UCSD: University of California, San Diego)H-Index: 1
#2Xiaodong Yan (UCSD: University of California, San Diego)H-Index: 10
Last.Navtej Toor (UCSD: University of California, San Diego)H-Index: 12
view all 7 authors...
Summary Group II introns are a class of retroelements that invade DNA through a copy-and-paste mechanism known as retrotransposition. Their coordinated activities occur within a complex that includes a maturase protein, which promotes splicing through an unknown mechanism. The mechanism of splice site exchange within the RNA active site during catalysis also remains unclear. We determined two cryo-EM structures at 3.6-A resolution of a group II intron reverse splicing into DNA. These structures ...
1 CitationsSource
#1Pratibha C. Koneru (CU: University of Colorado Boulder)H-Index: 4
#2Ashwanth C. Francis (Emory University)H-Index: 5
Last.Mamuka Kvaratskhelia (CU: University of Colorado Boulder)H-Index: 34
view all 15 authors...
HIV-1 inserts its genetic code into human genomes, turning healthy cells into virus factories. To do this, the virus uses an enzyme called integrase. Front-line treatments against HIV-1 called “integrase strand-transfer inhibitors” stop this enzyme from working. These inhibitors have helped to revolutionize the treatment of HIV/AIDS by protecting the cells from new infections. But, the emergence of drug resistance remains a serious problem. As the virus evolves, it changes the shape of its integ...
2 CitationsSource
#1Dmitry Lyumkis (Salk Institute for Biological Studies)H-Index: 18
#2Philip R Baldwin (Salk Institute for Biological Studies)H-Index: 3
Virtually every single-particle cryo-EM experiment currently suffers from specimen adherence to the air-water interface, leading to a non-uniform distribution in the set of projection views. Whereas it is well accepted that uniform projection distributions can lead to high-resolution reconstructions, non-uniform (anisotropic) distributions can negatively affect map quality, elongate structural features, and in some cases, prohibit interpretation altogether. Although some consequences of non-unif...
Source
#1Pratibha C. Koneru (CU: University of Colorado Boulder)H-Index: 4
#2Ashwanth C. Francis (Emory University)H-Index: 5
Last.Mamuka Kvaratskhelia (CU: University of Colorado Boulder)H-Index: 34
view all 15 authors...
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