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Making science a desirable career
2014
Science
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Polka and Kristin A. Krukenberg are organizers of the Future of Research Symposium held in Boston in early October and corresponding authors for the resulting report. ...
Polka and Kristin A. KrukenbergPublished by AAASon July 23, 2018 http://science.sciencemag.org/ Downloaded from Making science a desirable career Jessica K. Polka and Kristin A. ...
doi:10.1126/science.caredit.a1400311
fatcat:2vmb64m33ve7lljidtvq7q4nrm
Logistics of Organizing the FOR Symposium
2014
The Winnover
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For instance, we planned to have introductory remarks, a keynote, a panel (10 minute talks followed by time for Q&A), and a SCIENCE AND SOCIETY ABSTRACT Organizing this symposium was a tremendous learning ...
This is a good time to establish a collaborative editing platform. ...
in the Future of Science 2014); (McDowell, Krukenberg and Polka, An open letter to AAAS journal "Science": Postdocs need to address "The Future of Research" 2014)).
) ...
doi:10.15200/winn.141697.77958
fatcat:iwt4liljgfddjmvbzjkvj55r44
Osmolyte-induced conformational changes in the Hsp90 molecular chaperone
2009
Protein Science
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Here we investigate this issue with the Hsp90 molecular chaperone, a large dimeric protein that populates a complex conformational equilibrium. ...
This approach shows how osmolytes affect a highly cooperative open/closed structural transition between two conformations that differ by a domain-domain interaction. ...
Acknowledgments A special thanks to the Agard lab for many helpful discussions and to G. Hura for help with the SAXS data collection. ...
doi:10.1002/pro.282
pmid:19890989
pmcid:PMC2817839
fatcat:4222uffspvc67n5a2x7wqm57sm
Conformational dynamics of the molecular chaperone Hsp90
2011
Quarterly Reviews of Biophysics (print)
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Structural analyses have shown that Hsp90 is a highly dynamic and flexible molecule that can adopt a wide variety of structurally distinct states. ...
Hsp90 affects the folding and activation of a wide variety of substrate proteins including many involved in signaling and regulatory processes. ...
demonstrated that a highly open conformation and a more closed conformation are populated in a pH-dependent manner ( Fig. 3b ) (Krukenberg et al. 2009b) . ...
doi:10.1017/s0033583510000314
pmid:21414251
pmcid:PMC5070531
fatcat:22lmg4zfqzd3xb6kgkrqqrc744
Basal Activity of a PARP1-NuA4 Complex Varies Dramatically across Cancer Cell Lines
2014
Cell Reports
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These findings present a pathway for PARP1 activation and a direct link between PARP1 and chromatin remodeling outside of the DNA damage response. ...
A discovered complex containing the NuA4 chromatin-remodeling complex and PARP1 was responsible for high basal PARP1 activity, and NuA4 subunits were required for this activity. ...
K.A.K. was a Fayez Sarofim Fellow of the Damon Runyon Cancer Research Foundation (DRG-2053-10). This work was supported by 1 K99 CA175176-01 (K.A.K.) and 5 P01 CA139980-04 (T.J.M.). ...
doi:10.1016/j.celrep.2014.08.009
pmid:25199834
pmcid:PMC4177365
fatcat:aokcuayrcjcg7gbulvsmdjy2fu
Extracellular Poly(ADP-Ribose) Is a Pro-inflammatory Signal for Macrophages
2015
Chemistry and Biology
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All known PAR biology is intracellular, but we suspected it might also play a role in cell-to-cell communication during inflammation. ...
We found that PAR activated cytokine release in human and mouse macrophages, a hallmark of innate immune activation, and determined structure-activity relationships. ...
Correspondence kristin_krukenberg@hms.harvard.edu
In Brief Krukenberg et al. found that extracellular poly(ADP-ribose) activated cytokine secretion and phagocytosis in human and mouse macrophages through ...
doi:10.1016/j.chembiol.2015.03.007
pmid:25865309
pmcid:PMC4409933
fatcat:vjg44g3he5g6xkshrddqhuknem
Intra- and Intermonomer Interactions Are Required to Synergistically Facilitate ATP Hydrolysis in Hsp90
2008
Journal of Biological Chemistry
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This loop contains hydrophobic residues as well as a critical arginine that provides a direct linkage to the ␥-phosphate of bound ATP. ...
Using the crystal structures as a guide, we examined the role of intra-and intermonomer interactions in stabilizing the ATPase activity of a single active site within an intact dimer. ...
Intermonomer (trans) activity ϭ ␣A 11 ϩ A 22 ϩ 0.5*␥ ͑A 12 ϩ A wt ͒ (Eq. 1) Intramonomer (cis) activity ϭ ␣A 11 ϩ A 22 ϩ 0.5*␥ ͑A 11 ϩ A 22 ͒ (Eq. 2) where ␣, , and ␥ represent the fraction homodimer ...
doi:10.1074/jbc.m800046200
pmid:18492664
pmcid:PMC2475720
fatcat:4te2saigr5gj5fyx6wkxlrxoyy
Multiple Conformations of E. coli Hsp90 in Solution: Insights into the Conformational Dynamics of Hsp90
2008
Structure
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These studies provide a unique view of Hsp90 conformational dynamics and provide a model for the role of nucleotide in effecting conformational change. ...
In solution, nucleotide-free HtpG adopts a more extended conformation than observed in the crystal, and upon the addition of AMPPNP, HtpG is in equilibrium between this open state and a closed state that ...
K.A.K. was supported by a NSDEG graduate fellowship. F.F. is grateful for a long-term fellowship from the Human Frontier Science Project Organization. ...
doi:10.1016/j.str.2008.01.021
pmid:18462680
pmcid:PMC2600884
fatcat:oloelqnfvfcttaixpycjepy6my
Grp94, the endoplasmic reticulum Hsp90, has a similar solution conformation to cytosolic Hsp90 in the absence of nucleotide
2009
Protein Science
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These results provide the first evidence that Grp94 shares a conformational state with other Hsp90 homologs. ...
This conformation differs from the yeast AMPPNP-bound crystal state, suggesting that Grp94 may have a different conformational cycle. ...
Apo HtpG exists in a pH-dependent conformational equilibrium between an open-extended state and a more closed state (Krukenberg et al., in press). ...
doi:10.1002/pro.191
pmid:19554567
pmcid:PMC2777357
fatcat:gcaof3qsuvfgrdozr5clrmrnfi
The conserved arginine 380 of Hsp90 is not a catalytic residue, but stabilizes the closed conformation required for ATP hydrolysis
2012
Protein Science
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to be a catalytic residue. ...
Hsp90, a dimeric ATP-dependent molecular chaperone, is required for the folding and activation of numerous essential substrate "client" proteins including nuclear receptors, cell cycle kinases, and telomerase ...
addition of saturating amounts of AMPPNP the bacterial and yeast SAXS curves exhibit a more narrow range of distances in their P(r) curves with a peak around 55 Å indicating a Figure 2 . ...
doi:10.1002/pro.2103
pmid:22653663
pmcid:PMC3537237
fatcat:twpnhwvdlve7pfso2gskkljq6q
chy1, anArabidopsisMutant with Impaired β-Oxidation, Is Defective in a Peroxisomal β-Hydroxyisobutyryl-CoA Hydrolase
2001
Journal of Biological Chemistry
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We have cloned CHY1, which appears to encode a peroxisomal protein 43% identical to a mammalian valine catabolic enzyme that hydrolyzes -hydroxyisobutyryl-CoA. ...
The Arabidopsis chy1 mutant is resistant to indole-3butyric acid, a naturally occurring form of the plant hormone auxin. ...
G to A mutation at position 518 (where the A of the initiator ATG is position 1; Fig. 3A ), chy1-2 has a 34-bp deletion from positions 1084 to 1118 (Fig. 3A) , and chy1-3 has a G to A mutation at position ...
doi:10.1074/jbc.m104679200
pmid:11404361
fatcat:l2sd4egh6jc3rgj7x6vllpqzsy
Integration of Small-Angle X-Ray Scattering Data into Structural Modeling of Proteins and Their Assemblies
2008
Journal of Molecular Biology
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The scoring function is optimized by a biased Monte Carlo protocol, including quasi-Newton and simulated annealing schemes. ...
A major challenge in structural biology is to determine the configuration of domains and proteins in multidomain proteins and assemblies, respectively. ...
RMSD (Å) Δr (Å) Δα (°) RMSD (Å) Δr (Å) Δα (°) RMSD (Å) Δr (Å) Δα (°) 1ha0 c We predicted domain configurations using protocols that differed by the initial configuration (near-template or RBNC) and the ...
doi:10.1016/j.jmb.2008.07.074
pmid:18694757
pmcid:PMC2745287
fatcat:ma3i7hrsgfg6fk4nn7wunwydlu
Shaping the Future of Research: a perspective from junior scientists
2015
F1000Research
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A group of postdocs in the Boston area who are invested in improving the scientific endeavor, planned a symposium held on October 2 and 3 , 2014, as a way to join the discussion about the future of US ...
Here we present a report of the proceedings of participant-driven workshops and the organizers' synthesis of the outcomes. ...
"For a lot of mentors, it's not a priority to engage in your career path". ...
doi:10.12688/f1000research.5878.2
pmid:25653845
pmcid:PMC4304227
fatcat:wiqe5j2omfaytdd7zpnbyy433i
Shaping the Future of Research: a perspective from junior scientists
2014
F1000Research
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A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
A group of postdocs in the Boston area who are invested in improving the scientific endeavor, planned a symposium held on October 2 and 3 , 2014, as a way to join the discussion about the future of US ...
Here we present a report of the proceedings of participant-driven workshops and the organizers' synthesis of the outcomes. ...
"For a lot of mentors, it's not a priority to engage in your career path". ...
doi:10.12688/f1000research.5878.1
fatcat:rqkcdxgjzne7lcttqrbfd4acmq
A method for integrative structure determination of protein-protein complexes
2012
Computer applications in the biosciences : CABIOS
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Results: Here, we present a combined approach that computationally integrates data from a variety of fast and accessible experimental techniques for rapid and accurate structure determination of protein-protein ...
The method is tested on a docking benchmark consisting of 176 known complex structures and simulated experimental data. ...
I-RMSD of 0-5 Å or L-RMSD of 0-15 Å ). ...
doi:10.1093/bioinformatics/bts628
pmid:23093611
pmcid:PMC3519461
fatcat:ck4vkfpaezcgtef4nfhbnwcfgu
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