An AMBER/DYANA/MOLMOL Phosphorylated Amino Acid Library Set and Incorporation into NMR Structure Calculations

2005 ◽  
Vol 33 (1) ◽  
pp. 15-24 ◽  
Author(s):  
John W. Craft ◽  
Glen B. Legge
1981 ◽  
Vol 194 (3) ◽  
pp. 1007-1009 ◽  
Author(s):  
J Schuck ◽  
G Reichert ◽  
O G Issinger

Four non-ribosomal proteins from native 40 S ribosomal subunits with mol.wts. of 110 000, 84 000, 68 000 and 26 000 were phosphorylated in vivo when ascites cells were incubated in the presence of [32P]Pi. The 110 000-, 84 000- and 26 000-dalton proteins are identical with phosphorylated products from native 40 S subunits after phosphorylation in vitro by a cyclic nucleotide-independent protein kinase. Phosphoserine was the major phosphorylated amino acid of the proteins phosphorylated in vivo and in vitro.


2007 ◽  
Vol 129 (4) ◽  
pp. 820-827 ◽  
Author(s):  
Daniel J. Mandell ◽  
Ilya Chorny ◽  
Eli S. Groban ◽  
Sergio E. Wong ◽  
Elisheva Levine ◽  
...  

2005 ◽  
Vol 31 (1) ◽  
pp. 21-34 ◽  
Author(s):  
Michele Fossi ◽  
Jens Linge ◽  
Dirk Labudde ◽  
Dietmar Leitner ◽  
Michael Nilges ◽  
...  

2002 ◽  
Vol 254 (2) ◽  
pp. 322-330 ◽  
Author(s):  
Johan Ekeroth ◽  
Annika Borgh ◽  
Peter Konradsson ◽  
Bo Liedberg

2006 ◽  
Vol 128 (23) ◽  
pp. 7566-7571 ◽  
Author(s):  
Eiso AB ◽  
David J. R. Pugh ◽  
Robert Kaptein ◽  
Rolf Boelens ◽  
Alexandre M. J. J. Bonvin

2015 ◽  
Vol 109 (3) ◽  
pp. 574-585 ◽  
Author(s):  
Ye Tian ◽  
Charles D. Schwieters ◽  
Stanley J. Opella ◽  
Francesca M. Marassi

2017 ◽  
Vol 95 (8) ◽  
pp. 830-836 ◽  
Author(s):  
John Justine S. Villar ◽  
Adrian Roy L. Valdez ◽  
David H. Setiadi ◽  
Béla Fiser ◽  
Béla Viskolcz ◽  
...  

The conformational potential energy surface (PES) of a molecule provides insights into the relative stability of the possible foldamers. However, the time and space complexity of electronic structure calculations, commonly used to generate PES, increases exponentially with an increasing number of atoms. The use of mathematical functions to model the topology of conformational PES is an alternative to more computer-intensive quantum chemical calculations, but the choice and complexity of functions used are crucial in achieving more accurate results. This paper presents a method to illustrate the topology of amino acid diamide PESs through a linear combination of a Fourier series and a mixture of Gaussian functions. Results yield a significantly small error, with an average RMSE of 4.9946 kJ mol−1 for all fits, which suggest that these functions may be used to represent the topology of the PESs, with around twofold order of magnitude decrease in computational time, with respect to DFT electronic structure calculations. This study ultimately aims to provide a foundation for a framework on building polypeptide PES from individual amino acid PESs.


2019 ◽  
Vol 317 (4) ◽  
pp. F789-F804 ◽  
Author(s):  
Venkatesh Deshpande ◽  
Anika Kao ◽  
Viswanathan Raghuram ◽  
Arnab Datta ◽  
Chung-Lin Chou ◽  
...  

Vasopressin controls water balance largely through PKA-dependent effects to regulate the collecting duct water channel aquaporin-2 (AQP2). Although considerable information has accrued regarding the regulation of water and solute transport in collecting duct cells, information is sparse regarding the signaling connections between PKA and transport responses. Here, we exploited recent advancements in protein mass spectrometry to perform a comprehensive, multiple-replicate analysis of changes in the phosphoproteome of native rat inner medullary collecting duct cells in response to the vasopressin V2 receptor-selective agonist 1-desamino-8D-arginine vasopressin. Of the 10,738 phosphopeptides quantified, only 156 phosphopeptides were significantly increased in abundance, and only 63 phosphopeptides were decreased, indicative of a highly selective response to vasopressin. The list of upregulated phosphosites showed several general characteristics: 1) a preponderance of sites with basic (positively charged) amino acids arginine (R) and lysine (K) in position −2 and −3 relative to the phosphorylated amino acid, consistent with phosphorylation by PKA and/or other basophilic kinases; 2) a greater-than-random likelihood of sites previously demonstrated to be phosphorylated by PKA; 3) a preponderance of sites in membrane proteins, consistent with regulation by membrane association; and 4) a greater-than-random likelihood of sites in proteins with class I COOH-terminal PDZ ligand motifs. The list of downregulated phosphosites showed a preponderance of those with proline in position +1 relative to the phosphorylated amino acid, consistent with either downregulation of proline-directed kinases (e.g., MAPKs or cyclin-dependent kinases) or upregulation of one or more protein phosphatases that selectively dephosphorylate such sites (e.g., protein phosphatase 2A). The phosphoproteomic data were used to create a web resource for the investigation of G protein-coupled receptor signaling and regulation of AQP2-mediated water transport.


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