Search Results - "Komives, A."

Frustration in biomolecules by Ferreiro, Diego U, Komives, Elizabeth A, Wolynes, Peter G

“…Biomolecules are the prime information processing elements of living matter. Most of these inanimate systems are polymers that compute their own structures and…”
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Site-specific identification and quantitation of endogenous SUMO modifications under native conditions by Lumpkin, Ryan J., Gu, Hongbo, Zhu, Yiying, Leonard, Marilyn, Ahmad, Alla S., Clauser, Karl R., Meyer, Jesse G., Bennett, Eric J., Komives, Elizabeth A.

“…Small ubiquitin-like modifier (SUMO) modification regulates numerous cellular processes. Unlike ubiquitin, detection of endogenous SUMOylated proteins is…”
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Single-molecule conformational dynamics of a transcription factor reveals a continuum of binding modes controlling association and dissociation by Chen, Wei, Lu, Wei, Wolynes, Peter G, Komives, Elizabeth A

“…Abstract Binding and unbinding of transcription factors to DNA are kinetically controlled to regulate the transcriptional outcome. Control of the release of…”
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Dynamic allostery in thrombin-a review by Komives, Elizabeth A

“…Thrombin is a serine protease that catalyzes a large number of different reactions including proteolytic cleave of fibrinogen to make the fibrin clot…”
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Charge State Coalescence During Electrospray Ionization Improves Peptide Identification by Tandem Mass Spectrometry by Meyer, Jesse G., A. Komives, Elizabeth

“…We report the effects of supercharging reagents dimethyl sulphoxide (DMSO) and m -nitrobenzyl alcohol ( m -NBA) applied to untargeted peptide identification,…”
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Molecular stripping in the NF-κB/IκB/DNA genetic regulatory network by Potoyan, Davit A., Zheng, Weihua, Komives, Elizabeth A., Wolynes, Peter G.

“…Genetic switches based on the NF-κB/IκB/DNA system are master regulators of an array of cellular responses. Recent kinetic experiments have shown that IκB can…”
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Surveying biomolecular frustration at atomic resolution by Chen, Mingchen, Chen, Xun, Schafer, Nicholas P., Clementi, Cecilia, Komives, Elizabeth A., Ferreiro, Diego U., Wolynes, Peter G.

“…To function, biomolecules require sufficient specificity of interaction as well as stability to live in the cell while still being able to move. Thermodynamic…”
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Calcium sensing by the STIM1 ER-luminal domain by Gudlur, Aparna, Zeraik, Ana Eliza, Hirve, Nupura, Rajanikanth, V., Bobkov, Andrey A., Ma, Guolin, Zheng, Sisi, Wang, Youjun, Zhou, Yubin, Komives, Elizabeth A., Hogan, Patrick G.

“…Stromal interaction molecule 1 (STIM1) monitors ER-luminal Ca 2+ levels to maintain cellular Ca 2+ balance and to support Ca 2+ signalling. The prevailing view…”
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Author Correction: Structure and dynamics of the ASB9 CUL-RING E3 Ligase by Lumpkin, Ryan J., Baker, Richard W., Leschziner, Andres E., Komives, Elizabeth A.

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Measurement of the neutron lifetime using a magneto-gravitational trap and in situ detection by Pattie, Jr, R W, Callahan, N B, Cude-Woods, C, Adamek, E R, Broussard, L J, Clayton, S M, Currie, S A, Dees, E B, Ding, X, Engel, E M, Fellers, D E, Fox, W, Geltenbort, P, Hickerson, K P, Hoffbauer, M A, Holley, A T, Komives, A, Liu, C-Y, MacDonald, S W T, Makela, M, Morris, C L, Ortiz, J D, Ramsey, J, Salvat, D J, Saunders, A, Seestrom, S J, Sharapov, E I, Sjue, S K, Tang, Z, Vanderwerp, J, Vogelaar, B, Walstrom, P L, Wang, Z, Wei, W, Weaver, H L, Wexler, J W, Womack, T L, Young, A R, Zeck, B A

“…The precise value of the mean neutron lifetime, τ , plays an important role in nuclear and particle physics and cosmology. It is used to predict the ratio of…”
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Structure and dynamics of the ASB9 CUL-RING E3 Ligase by Lumpkin, Ryan J., Baker, Richard W., Leschziner, Andres E., Komives, Elizabeth A.

“…The Cullin 5 (CUL5) Ring E3 ligase uses adaptors Elongins B and C (ELOB/C) to bind different SOCS-box-containing substrate receptors, determining the substrate…”
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On the role of frustration in the energy landscapes of allosteric proteins by Ferreiro, Diego U, Hegler, Joseph A, Komives, Elizabeth A, Wolynes, Peter G

“…Natural protein domains must be sufficiently stable to fold but often need to be locally unstable to function. Overall, strong energetic conflicts are…”
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Serine protease dynamics revealed by NMR analysis of the thrombin-thrombomodulin complex by Peacock, Riley B., McGrann, Taylor, Tonelli, Marco, Komives, Elizabeth A.

“…Serine proteases catalyze a multi-step covalent catalytic mechanism of peptide bond cleavage. It has long been assumed that serine proteases including thrombin…”
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The homeodomain regulates stable DNA binding of prostate cancer target ONECUT2 by Chatterjee, Avradip, Gallent, Brad, Katiki, Madhusudhanarao, Qian, Chen, Harter, Matthew R., Silletti, Steve, Komives, Elizabeth A., Freeman, Michael R., Murali, Ramachandran

“…The CUT and homeodomain are ubiquitous DNA binding elements often tandemly arranged in multiple transcription factor families. However, how the CUT and…”
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Allosteric networks in thrombin distinguish procoagulant vs. anticoagulant activities by Gasper, Paul M., Fuglestad, Brian, Komives, Elizabeth A., Markwick, Phineus R. L., McCammon, J. Andrew

“…The serine protease α-thrombin is a dual-action protein that mediates the blood-clotting cascade. Thrombin alone is a procoagulant, cleaving fibrinogen to make…”
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Localizing frustration in native proteins and protein assemblies by Ferreiro, Diego U, Hegler, Joseph A, Komives, Elizabeth A, Wolynes, Peter G

“…We propose a method of quantifying the degree of frustration manifested by spatially local interactions in protein biomolecules. This method of localization…”
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Identification of high levels of phytochelatins, glutathione and cadmium in the phloem sap of Brassica napus. A role for thiol-peptides in the long-distance transport of cadmium and the effect of cadmium on iron translocation by Mendoza-Cózatl, David G, Butko, Emerald, Springer, Franziska, Torpey, Justin W, Komives, Elizabeth A, Kehr, Julia, Schroeder, Julian I

“…Phytochelatins (PCs) are glutathione-derived peptides that function in heavy metal detoxification in plants and certain fungi. Recent research in Arabidopsis…”
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Target binding triggers hierarchical phosphorylation of human Argonaute-2 to promote target release by Bibel, Brianna, Elkayam, Elad, Silletti, Steve, Komives, Elizabeth A, Joshua-Tor, Leemor

“…Argonaute (Ago) proteins play a central role in post-transcriptional gene regulation through RNA interference (RNAi). Agos bind small RNAs (sRNAs) including…”
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Active site remodeling in tumor-relevant IDH1 mutants drives distinct kinetic features and potential resistance mechanisms by Mealka, Matthew, Sierra, Nicole A., Avellaneda Matteo, Diego, Albekioni, Elene, Khoury, Rachel, Mai, Timothy, Conley, Brittany M., Coleman, Nalani J., Sabo, Kaitlyn A., Komives, Elizabeth A., Bobkov, Andrey A., Cooksy, Andrew L., Silletti, Steve, Schiffer, Jamie M., Huxford, Tom, Sohl, Christal D.

“…Mutations in human isocitrate dehydrogenase 1 (IDH1) drive tumor formation in a variety of cancers by replacing its conventional activity with a neomorphic…”
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The Dynamic Structure of Thrombin in Solution by Fuglestad, Brian, Gasper, Paul M., Tonelli, Marco, McCammon, J. Andrew, Markwick, Phineus R.L., Komives, Elizabeth A.

“…The backbone dynamics of human α-thrombin inhibited at the active site serine were analyzed using R1, R2, and heteronuclear NOE experiments, variable…”
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