Rosetta3

Leaver‐Fay, Andrew; Tyka, Michael D.; Lewis, Steven M.; Lange, Oliver; Thompson, James; Jacak, Ron; Kaufman, Kristian W.; Renfrew, P. Douglas; Smith, Colin A.; Sheffler, Will; Davis, Ian; Cooper, Seth; Treuille, Adrien; Mandell, Daniel J.; Richter, Florian; Ban, Yih-En Andrew; Fleishman, Sarel J.; Corn, Jacob E.; Kim, David E.; Lyskov, Sergey; Berrondo, Monica; Mentzer, Stuart; Popović, Zoran; Havranek, James J.; Karanicolas, John; Das, Rhiju; Meiler, Jens; Kortemme, Tanja; Gray, Jeffrey J.; Kuhlman, Brian; Baker, David; Bradley, Philip

doi:10.1016/b978-0-12-381270-4.00019-6

Cited by 1,630 publications

(877 citation statements)

References 43 publications

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“…Further prediction of folding was performed using Rosetta (44). Two sequences within the Linker1 region were selected: Spt5 residues 433 to 511, covering the entire Linker1, and a shorter sequence, 460 to 511, with a lower degree of disorder based on the disorder prediction.…”

Section: Recombinant Proteinsmentioning

confidence: 99%

Structures and Functions of the Multiple KOW Domains of Transcription Elongation Factor Spt5

Meyer

Zhang

et al. 2015

Molecular and Cellular Biology

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The eukaryotic Spt4-Spt5 heterodimer forms a higher-order complex with RNA polymerase II (and I) to regulate transcription elongation. Extensive genetic and functional data have revealed diverse roles of Spt4-Spt5 in coupling elongation with chromatin modification and RNA-processing pathways. A mechanistic understanding of the diverse functions of Spt4-Spt5 is hampered by challenges in resolving the distribution of functions among its structural domains, including the five KOW domains in Spt5, and a lack of their high-resolution structures. We present high-resolution crystallographic results demonstrating that distinct structures are formed by the first through third KOW domains (KOW1-Linker1 [K1L1] and KOW2-KOW3) of Saccharomyces cerevisiae Spt5. The structure reveals that K1L1 displays a positively charged patch (PCP) on its surface, which binds nucleic acids in vitro, as shown in biochemical assays, and is important for in vivo function, as shown in growth assays. Furthermore, assays in yeast have shown that the PCP has a function that partially overlaps that of Spt4. Synthesis of our results with previous evidence suggests a model in which Spt4 and the K1L1 domain of Spt5 form functionally overlapping interactions with nucleic acids upstream of the transcription bubble, and this mechanism may confer robustness on processes associated with transcription elongation.T ranscription by RNA polymerase (RNAP) II is a regulated process that requires over 60 different accessory factors that interact dynamically with the polymerase as it proceeds through the three main stages of transcription: initiation, elongation, and termination (1). Each RNAP II complex is structurally and biochemically tuned to cope with a set of conditions (e.g., the chromatin state) and to accomplish specific functions (e.g., promoter-dependent initiation) associated with a particular stage of transcription. In eukaryotes, the processes of RNAP II elongation and termination interact closely with pathways of pre-mRNA processing, 3=-end formation, and RNA export (2-4) and thus form temporally and spatially coupled activities that together determine transcriptional responses to intrinsic and extrinsic signaling and regulate RNA metabolism. The heterodimeric complex of Spt4-Spt5 is one of several protein factors that participate in all of the steps that follow transcription initiation. Saccharomyces cerevisiae Spt4-Spt5 is known to coordinate transcription elongation with chromatin remodeling and histone modification; it functions as a general elongation factor for both RNAP II and RNAP I and coordinates with 5= capping, splicing, and 3=-end processing of transcripts (reviewed by Hartzog and Fu [5]). The metazoan homolog of Spt4-Spt5, DSIF, partners with NELF and additional RNAP IIassociated complexes (e.g., P-TEFb and Mediator) to impart a pause-and-release mechanism that regulates RNAP II activity during the initiation-to-elongation transition near promoterproximal regions (6-8). While facilitative for transcription elongation, Spt4-Spt5 also pl...

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Section: Recombinant Proteinsmentioning

confidence: 99%

Structures and Functions of the Multiple KOW Domains of Transcription Elongation Factor Spt5

Meyer

Zhang

et al. 2015

Molecular and Cellular Biology

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“…The correlation diminishes at 240 and 300 K, presumably because other effects become more important. design and folding (Leaver-Fay et al, 2011). RosettaHoles generates 'packing scores' for each residue based upon the amount of void volume around its atoms.…”

Section: Local Packingmentioning

confidence: 99%

Spatial distribution of radiation damage to crystalline proteins at 25–300 K

Warkentin

Badeau

Hopkins

et al. 2012

Acta Crystallogr D Biol Cryst

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The spatial distribution of radiation damage (assayed by increases in atomic B factors) to thaumatin and urease crystals at temperatures ranging from 25 to 300 K is reported. The nature of the damage changes dramatically at approximately 180 K. Above this temperature the role of solvent diffusion is apparent in thaumatin crystals, as solvent-exposed turns and loops are especially sensitive. In urease, a flap covering the active site is the most sensitive part of the molecule and nearby loops show enhanced sensitivity. Below 180 K sensitivity is correlated with poor local packing, especially in thaumatin. At all temperatures, the component of the damage that is spatially uniform within the unit cell accounts for more than half of the total increase in the atomic B factors and correlates with changes in mosaicity. This component may arise from lattice-level, rather than local, disorder. The effects of primary structure on radiation sensitivity are small compared with those of tertiary structure, local packing, solvent accessibility and crystal contacts.

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“…This sequence alignment was used to thread the A3F sequence onto the A3G crystal structure. In a two-step procedure, loop regions missing from the 3V4K structure were constructed, the A3F model was relaxed, and A3F loops then were rebuilt to sample a larger conformational space (36,37,39). Twenty thousand candidate models were generated initially.…”

Section: Methodsmentioning

confidence: 99%

“…An A3F model was built using Rosetta 3.3, a software suite for predicting and designing protein structures, protein folding mechanisms, and protein-protein interactions (36). The 1.38-Å-resolution structure of A3G, Protein Data Bank (PDB) entry 3V4K (37), was used to build this model in order to gain more information about amino acid side chains than is present in the published structure of a modified A3F C-terminal CD domain, PDB entry 4IOU (38).…”

Section: Methodsmentioning

confidence: 99%