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Making science a desirable career

Jessica K. Polka, Kristin A. Krukenberg
2014 Science  
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

Sarah A. Mazzilli, Kearney T. W. Gunsalus, Gary S. McDowell, Kristin A. Krukenberg, Jessica K. Polka
2014 The Winnover  
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

Timothy O. Street, Kristin A. Krukenberg, Jörg Rosgen, D. Wayne Bolen, David A. Agard
2009 Protein Science  
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

Kristin A. Krukenberg, Timothy O. Street, Laura A. Lavery, David A. Agard
2011 Quarterly Reviews of Biophysics (print)  
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

Kristin A. Krukenberg, Ruomu Jiang, Judith A. Steen, Timothy J. Mitchison
2014 Cell Reports  
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

Kristin A. Krukenberg, Sujeong Kim, Edwin S. Tan, Zoltan Maliga, Timothy J. Mitchison
2015 Chemistry and Biology  
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

Christian N. Cunningham, Kristin A. Krukenberg, David A. Agard
2008 Journal of Biological Chemistry  
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

Kristin A. Krukenberg, Friedrich Förster, Luke M. Rice, Andrej Sali, David A. Agard
2008 Structure  
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

Kristin A. Krukenberg, Ulrike M. K. Böttcher, Daniel R. Southworth, David A. Agard
2009 Protein Science  
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

Christian N. Cunningham, Daniel R. Southworth, Kristin A. Krukenberg, David A. Agard
2012 Protein Science  
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

Bethany K. Zolman, Melanie Monroe-Augustus, Beth Thompson, John W. Hawes, Kristin A. Krukenberg, Seiichi P. T. Matsuda, Bonnie Bartel
2001 Journal of Biological Chemistry  
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

Friedrich Förster, Benjamin Webb, Kristin A. Krukenberg, Hiro Tsuruta, David A. Agard, Andrej Sali
2008 Journal of Molecular Biology  
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

Gary S. McDowell, Kearney T. W. Gunsalus, Drew C. MacKellar, Sarah A. Mazzilli, Vaibhav P. Pai, Patricia R. Goodwin, Erica M. Walsh, Avi Robinson-Mosher, Thomas A. Bowman, James Kraemer, Marcella L. Erb, Eldi Schoenfeld (+6 others)
2015 F1000Research  
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

Gary S. McDowell, Kearney T. W. Gunsalus, Drew C. MacKellar, Sarah A. Mazzilli, Vaibhav P. Pai, Patricia R. Goodwin, Erica M. Walsh, Avi Robinson-Mosher, Thomas A. Bowman, James Kraemer, Marcella L. Erb, Eldi Schoenfeld (+6 others)
2014 F1000Research  
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

Dina Schneidman-Duhovny, Andrea Rossi, Agustin Avila-Sakar, Seung Joong Kim, Javier Velázquez-Muriel, Pavel Strop, Hong Liang, Kristin A. Krukenberg, Maofu Liao, Ho Min Kim, Solmaz Sobhanifar, Volker Dötsch (+5 others)
2012 Computer applications in the biosciences : CABIOS  
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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