25 papers · ranked by Valyu relevance
Iman Tavassoly, Adel Mehrpooya, Parsa Mirlohi, Zahra Abbaspourasadollah
- 1. QMed Insights, New York, NY, USA - 2. School of Mathematical Sciences, Faculty of Science, Queensland University of Technology (QUT), 2 George Street, Brisbane, 4000, Queensland, Australia - 3. Max Planck Queensland Centre for the Materials Science of Extracellular Matrices, Brisbane, Queensland, Australia - 4.…
S. Marjan Varedi K., Alejandra C. Ventura, Sofia D. Merajver, Xiaoxia Nina Lin + 1 more
Phosphorylation-triggered degradation is a common strategy for elimination of regulatory proteins in many important cell signaling processes. Interesting examples include cyclin-dependent kinase inhibitors such as p27 in human and Sic1 in yeast, which play crucial roles during the G1/S transition in the cell cycle. In…
Thapanar Suwanmajo, Vaidhiswaran Ramesh, J. Krishnan
Multisite phosphorylation (and generally multisite modification) is a basic way of encoding substrate function and circuits/networks of post-translational modifications (PTM) are ubiquitous in cell signalling. The information processing characteristics of PTM systems are a focal point of broad interest. The ordering of…
Germán Enciso, Douglas R. Kellogg, Arturo Vargas, Jorg Stelling
We explore a framework to model the dose response of allosteric multisite phosphorylation proteins using a single auxiliary variable. This reduction can closely replicate the steady state behavior of detailed multisite systems such as the Monod-Wyman-Changeux allosteric model or rule-based models. Optimal…
Carlo Chan, Xinfeng Liu, Liming Wang, Lee Bardwell + 3 more
'Germán Enciso' 'Jorg Stelling'] The phosphorylation of a substrate at multiple sites is a common protein modification that can give rise to important structural and electrostatic changes. Scaffold proteins can enhance protein phosphorylation by facilitating an interaction between a protein kinase enzyme and its target…
Guangyan Qing, Qi Lu, Xiuling Li, Jing Liu + 3 more
'Xinmiao Liang' 'Taolei Sun'] Multisite phosphorylation is an important and common mechanism for finely regulating protein functions and subsequent cellular responses. However, this study is largely restricted by the difficulty to capture low-abundance multiply phosphorylated peptides (MPPs) from complex biosamples…
Carsten Conradi, Anne Shiu
Multisite phosphorylation plays an important role in intracellular signaling. There has been much recent work aimed at understanding the dynamics of such systems when the phosphorylation/dephosphorylation mechanism is distributive, that is, when the binding of a substrate and an enzyme molecule results in addition or…
Minghan Chen, Mansooreh Ahmadian, Layne T. Watson, Yang Cao
Multisite phosphorylation plays an important role in regulating switchlike protein activity and has been used widely in mathematical models. With the development of new experimental techniques and more molecular data, molecular phosphorylation processes emerge in many systems with increasing complexity and sizes. These…
Ildar I. Sadreev, Michael Z. Q. Chen, Gavin I. Welsh, Yoshinori Umezawa + 3 more
'Yoshinori Umezawa' 'Nikolay V. Kotov' 'Najl V. Valeyev' 'Gautam Sethi'] Phosphorylation is a fundamental biochemical reaction that modulates protein activity in cells. While a single phosphorylation event is relatively easy to understand, multisite phosphorylation requires systems approaches for deeper elucidation of…
Carsten Conradi, Anne Shiu
Post-translational modification (PTM) of proteins is important for signal transduction, and hence significant effort has gone toward understanding how PTM networks process information. This involves, on the theory side, analyzing the dynamical systems arising from such networks. Which networks are, for instance…
Christopher A. Waudby, Saul Alvarez-Teijeiro, Simon Suppinger, Paul R. Brown + 3 more
Protein phosphorylation is a major regulatory mechanism of cellular signalling. The c-Jun proto-oncoprotein is phosphorylated at four residues within its transactivation domain (TAD) by the JNK family kinases, but the functional significance of c-Jun multisite phosphorylation has remained elusive. Here we show that…
Katharina Holstein, Dietrich Flockerzi, Carsten Conradi
Multisite phosphorylation networks are encountered in many intracellular processes like signal transduction, cell-cycle control or nuclear signal integration. In this contribution networks describing the phosphorylation and dephosphorylation of a protein at n sites in a sequential distributive mechanism are considered.…
Elizabeth A. Libby, Shlomi Reuveni, Jonathan Dworkin
Isogenic populations of cells exhibit phenotypic variability that has specific physiological consequences. For example, individual bacteria within a population can differ in their sensitivity to an antibiotic, but whether this variability can be regulated or is generally an unavoidable consequence of stochastic…
Jonathan B. Asfaha, Mihkel Örd, Christopher R. Carlson, Ilona Faustova + 2 more
Cell-cycle progression is driven by the phosphorylation of cyclin-dependent kinase (Cdk) substrates^1–3^. The order of substrate phosphorylation depends in part on the general rise in Cdk activity during the cell cycle^4–7^, together with variations in substrate docking to sites on associated cyclin and Cks subunits^3…
Michelle M. Conti, Rui Li, Michelle A. Narváez Ramos, Lihua Julie Zhu + 2 more
Ordered cell cycle progression is coordinated by cyclin dependent kinases (CDKs). CDKs often phosphorylate substrates at multiple sites clustered within disordered regions. However, for most substrates, it is not known which phosphosites are functionally important. We developed a high-throughput approach, Phosphosite…
Aymen al-Rawi, Svitlana Korolchuk, Jane Endicott, Tony Ly
Ordered protein phosphorylation by CDKs is a key mechanism for regulating the cell cycle. How temporal order is enforced in mammalian cells remains unclear. Using a fixed cell kinase assay and phosphoproteomics, we show how CDK1 activity and non-catalytic CDK1 subunits contribute to the choice of substrate and site of…
Teng Wang, Chenzi Jin, Fangting Li
Fission yeast G2/M transition is regulated by a biochemical reaction networks which contains four components: Cdc13, Cdc2, Wee1, and Cdc25. This circuit is characterized by the ultrasensitive responses of Wee1 or Cdc25 to Cdc13/Cdc2 activity, and the bistability of Cdc2 activation. Previous work has shown that this…
Henry Y. Ng, Devon H. Whelpley, Armin N. Adly, Robert A. Maxwell + 1 more
Cell cycle progression is governed by complexes of the cyclin-dependent kinases (CDKs) and their regulatory subunits cyclin and Cks1. CDKs phosphorylate hundreds of substrates, often at multiple sites. Multisite phosphorylation depends on Cks1, which binds initial priming phosphorylation sites to promote secondary…
Arriën Symon Rauh, Gustav Stausbøll Hedemark, Giulio Tesei, Kresten Lindorff-Larsen
Protein phosphorylation is a common and essential post-translational modification that affects biochemical properties and regulates biological activities. Phosphorylation is particularly common for intrinsically disordered proteins and can significantly modulate their function and potential to interact with binding…
Anil Incel, Sudhirkumar Shinde, Ignacio A. Diez, Maria M. Stollenwerk + 2 more
Immunoaffinity enrichment based on antipeptide antibodies coupled to mass spectrometry-based identification and quantification (immuno-MS) is a promising approach to translate proteomics to clinical assays with diagnostic value. This is linked to precision cancer medicine, where immuno-MS based studies of protein…
Zeyu Yang, Steve Marston, ian gould
Phosphorylation of cardiac muscle troponin I by protein kinase A enhances troponin regulatory dynamics and is an essential part of the’ flight or fight’ response to adrenaline. Elucidating how phosphorylation at serines 22 and 23 modulates structural dynamics has been difficult as key regulatory segments of troponin…
John P. Stoppelman, Tracey T. Ng, Paul S. Nerenberg, Lee-Ping Wang
Phosphorylation of select amino acid residues is one of the most common tools for regulating protein structure and function. While computational modeling can be used to explore the detailed structural changes associated with phosphorylation, most molecular mechanics force fields developed for the simulation of…
wenzhong liu, hualan li
Increased vascular permeability is a characteristic of Hantavirus illness, for which there is now no treatment. We employed the domain search method to investigate the Hantavirus protein in this present work. The results indicated that the membrane glycoprotein E protein (containing Gn-Gc) of Hantavirus had lipid…
Ankita Tripathi, Kshatresh Dubey
L-Homoserine Kinase is crucial in the biosynthesis of Threonine, Isoleucine, and Methionine. Using computational tools herein, we provide new insight into the catalytic mechanism of L-homoserine kinase, showing a direct involvement of H139 as a catalytic base, in contrast to the previous consensus, where no involvement…
Suk ho Hong, Sarah Y Xi, Andrew C Johns, Lauren C Tang + 3 more
Protein tyrosine phosphatases (PTPs) are an important class of enzymes that modulate essential cellular processes through protein dephosphorylation and are dysregulated in various disease states. There is demand for new compounds that target the active sites of these enzymes, for use as chemical tools to dissect their…