scholarly journals Why nature chose phosphate to modify proteins

2012 ◽  
Vol 367 (1602) ◽  
pp. 2513-2516 ◽  
Author(s):  
Tony Hunter
Keyword(s):  
Hydrogen Bonds ◽  
Chemical Properties ◽  
Phosphate Ester ◽  
Salt Bridges ◽  
Post Translational Modification ◽  
Protein Protein Interaction ◽  
Binding Domains ◽  
Phosphate Diester ◽  
Hydroxyamino Acids ◽  
Inducible Protein

The advantageous chemical properties of the phosphate ester linkage were exploited early in evolution to generate the phosphate diester linkages that join neighbouring bases in RNA and DNA (Westheimer 1987 Science 235 , 1173–1178). Following the fixation of the genetic code, another use for phosphate ester modification was found, namely reversible phosphorylation of the three hydroxyamino acids, serine, threonine and tyrosine, in proteins. During the course of evolution, phosphorylation emerged as one of the most prominent types of post-translational modification, because of its versatility and ready reversibility. Phosphoamino acids generated by protein phosphorylation act as new chemical entities that do not resemble any natural amino acid, and thereby provide a means of diversifying the chemical nature of protein surfaces. A protein-linked phosphate group can form hydrogen bonds or salt bridges either intra- or intermolecularly, creating stronger hydrogen bonds with arginine than either aspartate or glutamate. The unique size of the ionic shell and charge properties of covalently attached phosphate allow specific and inducible recognition of phosphoproteins by phosphospecific-binding domains in other proteins, thus promoting inducible protein–protein interaction. In this manner, phosphorylation serves as a switch that allows signal transduction networks to transmit signals in response to extracellular stimuli.

Identification of two independent nucleosome-binding domains in the transcriptional co-activator SPBP

2012 ◽  
Vol 442 (1) ◽  
pp. 65-75 ◽  
Author(s):  
Sagar Darvekar ◽  
Sylvia Sagen Johnsen ◽  
Agnete Bratsberg Eriksen ◽  
Terje Johansen ◽  
Eva Sjøttem
Keyword(s):  
Transcription Factors ◽  
Dependent Manner ◽  
Chromatin Binding ◽  
Binding Region ◽  
Interaction Domain ◽  
Binding Domains ◽  
Element Binding Protein ◽  
Inducible Protein ◽  
Responsive Element ◽  
Nucleosome Binding

Transcriptional regulation requires co-ordinated action of transcription factors, co-activator complexes and general transcription factors to access specific loci in the dense chromatin structure. In the present study we demonstrate that the transcriptional co-regulator SPBP [stromelysin-1 PDGF (platelet-derived growth factor)-responsive element binding protein] contains two independent chromatin-binding domains, the SPBP-(1551–1666) region and the C-terminal extended PHD [ePHD/ADD (extended plant homeodomain/ATRX-DNMT3-DNMT3L)] domain. The region 1551–1666 is a novel core nucleosome-interaction domain located adjacent to the AT-hook motif in the DNA-binding domain. This novel nucleosome-binding region is critically important for proper localization of SPBP in the cell nucleus. The ePHD/ADD domain associates with nucleosomes in a histone tail-dependent manner, and has significant impact on the dynamic interaction between SPBP and chromatin. Furthermore, SPBP and its homologue RAI1 (retinoic-acid-inducible protein 1), are strongly enriched on chromatin in interphase HeLa cells, and both proteins display low nuclear mobility. RAI1 contains a region with homology to the novel nucleosome-binding region SPBP-(1551–1666) and an ePHD/ADD domain with ability to bind nucleosomes. These results indicate that the transcriptional co-regulator SPBP and its homologue RAI1 implicated in Smith–Magenis syndrome and Potocki–Lupski syndrome both belong to the expanding family of chromatin-binding proteins containing several domains involved in specific chromatin interactions.

scholarly journals Synergistic Action of Prolactin (PRL) and Androgen on PRL-Inducible Protein Gene Expression in Human Breast Cancer Cells: A Unique Model for Functional Cooperation between Signal Transducer and Activator of Transcription-5 and Androgen Receptor

2002 ◽  
Vol 16 (7) ◽  
pp. 1696-1710 ◽  
Author(s):  
Jean-Louis Carsol ◽  
Sébastien Gingras ◽  
Jacques Simard
Keyword(s):  
Androgen Receptor ◽  
Reporter Gene ◽  
Potential Interaction ◽  
Site Directed Mutagenesis ◽  
Signal Transducer ◽  
Human Breast ◽  
Maximal Increase ◽  
Binding Domains ◽  
Inducible Protein ◽  
Half Site

Abstract The signal transducer and activator of transcription 5 (Stat5) has been shown to cooperate with some nuclear receptors. However, an interaction has never been demonstrated with the androgen receptor (AR). Given that the PRL-inducible protein/gross cystic disease fluid-15 (PIP/GCDFP-15) is both a PRL-controlled and an androgen-controlled protein, we used its promoter region to investigate the potential interaction between Stat5 and androgen receptor. Dihydrotestosterone or PRL alone slightly modulated or did not modulate the luciferase activity of all reporter gene constructs. In contrast, a maximal increase was observed using the −1477+42 reporter gene construct after exposure to both dihydrotestosterone and PRL. The requirement of half-site androgen-responsive elements and two consensus Stat5-binding elements, Stat5#1 and Stat5#2, was determined by site-directed mutagenesis. Activated Stat5B binds with a higher affinity to Stat5#2 than to Stat5#1. Stat5AΔ749 and Stat5BΔ754 mutants demonstrated that the Stat5 trans-activation domain is involved in the hormonal cooperation. The cooperation depends on the PRL-induced phosphorylation on Tyr694 in Stat5A and Tyr699 in Stat5B, as demonstrated using the Stat5AY694F and Stat5BY699F proteins. The use of AR Q798E, C619Y, and C784Y mutants showed that trans-activation, DNA-binding, and ligand-binding domains of AR are essential. Our study thus suggests a functional cooperation between AR and Stat5.

scholarly journals Charge density studies on 1:1 co-crystals of ethenzamide and saccharin

2014 ◽  
Vol 70 (a1) ◽  
pp. C964-C964
Author(s):  
Lucy Mapp ◽  
Mateusz Pitak ◽  
Simon Coles ◽  
Srinivasulu Aitipamula
Keyword(s):  
Hydrogen Bonds ◽  
Charge Density ◽  
Crystal Engineering ◽  
Chemical Properties ◽  
Secondary Level ◽  
Crystal Form ◽  
Monoclinic Space Group ◽  
Stoichiometric Ratio ◽  
Distribution Analysis ◽  
Space Group

The study of multi-component crystals, as well as the phenomenon of polymorphism, both have relevance to crystal engineering. Obtaining a specific polymorph is crucial as different polymorphs usually exhibit different physical and chemical properties and often the origin of this behaviour is unknown. This is especially important in the pharmaceutical industry. Herein, we present results of comparative studies of an analgesic drug, ethenzamide and its co-crystals with saccharin. The co-crystalisation of ethenzamide (2-ethoxybenzamide, EA) with saccharin (1,1-dioxo-,1,2-benzothiazol-3-one, SAC) with a 1:1 stoichiometric ratio resulted in two polymorphic forms of the co-crystal. Form I crystallises in the triclinic P-1 space group, whereas form II crystallises in monoclinic space group P21/n. Previous crystal structure analyses on forms I and II revealed that in both polymorphs the primary carboxy-amide-imide heterosynthon is the same, however the secondary level of interactions which extends the hydrogen bond network is different. Form I consists of extended linear tapes via N-H···O hydrogen bonds, whereas form II is composed of stacks of tetrameric motifs including N-H···O hydrogen bonds and C-H···O interactions. These two forms of EA-SAC can be classified as synthon polymorphs at a secondary level of hydrogen bonding [1]. In our approach an accurate, high resolution charge density distribution analysis has been carried out to obtain greater insight into the electronic structures of both types of the EA-SAC co-crystals and relate differences in electronic distribution with their polymorphic behaviour. To describe the nature and role of inter and intra-molecular interactions in a quantitative manner, the Hansen-Coppens formalism [2] and Bader's AIM theory [3] approach have been applied.

scholarly journals Structural and Functional Consequences of Age-Related Isomerization in α-Crystallins

2018 ◽  
Author(s):  
Yana A. Lyon ◽  
Dylan L. Riggs ◽  
Miranda P. Collier ◽  
Matteo T. Degiacomi ◽  
Justin L.P. Benesch ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Molecular Dynamics ◽  
Amino Acid ◽  
Native Mass Spectrometry ◽  
Salt Bridges ◽  
Loss Of Function ◽  
Post Translational Modification ◽  
Age Related ◽  
Αb Crystallin ◽  
Functional Consequences

AbstractLong-lived proteins are subject to spontaneous degradation and may accumulate a range of modifications over time, including subtle alterations such as isomerization. Recently, tandem-mass spectrometry approaches have enabled the identification and detailed characterization of such peptide isomers, including those differing only in chirality. However, the structural and functional consequences of these perturbations remain largely unexplored. Here we examine the site-specific impact of isomerization of aspartic acid and epimerization of serine in human αA- and αB-crystallin. From a total of 81 sites of modification identified in aged eye lenses, four (αBSer59, αASer162, αBAsp62, αBAsp109) map to crucial oligomeric interfaces. To characterize the effect of isomerization on quaternary assembly, molecular dynamics calculations and native mass spectrometry experiments were performed on recombinant forms of αA- and αB-crystallin that incorporate, or mimic, isomerized residues. In all cases, oligomerization is significantly affected, with epimerization of a single serine residue (αASer162) sufficing to weaken inter-subunit binding dramatically. Furthermore, phosphorylation of αBSer59, known to play an important regulatory role in oligomerization, is severely inhibited by serine epimerization and altered by isomerization of nearby αBAsp62. Similarly, isomerization of αBAsp109 disrupts a vital salt-bridge with αBArg120, a loss previously shown to yield aberrant oligomerization and aggregation in several disease variants. Our results illustrate how isomerization of amino-acid residues, which may seem like a minor structural perturbation, can have profound consequences on protein assembly and activity by disrupting specific hydrogen bonds and salt bridges.Significance StatementProteins play numerous critical roles in our bodies but suffer damage with increasing age. For example, isomerization is a spontaneous post-translational modification that alters the three-dimensional connectivity of an amino acid, yet remains invisible to traditional proteomic experiments. Herein, radical-based fragmentation was used for isomer identification while molecular dynamics and native mass spectrometry were utilized to assess structural consequences. The results demonstrate that isomerization disrupts both oligomeric assembly and phosphorylation in the α-crystallins, which are long-lived proteins in the lens of the eye. The loss of function associated with these modifications is likely connected to age-related diseases such as cataract and neurodegenerative disorders, while the methodologies we present represent a framework for structure-function studies on other isomerized proteins.

Effect of Non-Solubilizing SDS Concentrations on High Affinity Ca2+ Binding and Steady State Phosphorylation by Inorganic Phosphate of the Sarcoplasmic Reticulum ATPase

1989 ◽  
Vol 44 (1-2) ◽  
pp. 139-152 ◽  
Author(s):  
Elisabeth Fassold ◽  
Wilhelm Hasselbach ◽  
Bernd Küchler
Keyword(s):  
Sarcoplasmic Reticulum ◽  
Inorganic Phosphate ◽  
Atp Hydrolysis ◽  
Mutual Exclusion ◽  
Chemical Properties ◽  
Cooperative Interaction ◽  
Hydrophobic Force ◽  
High Affinity ◽  
Binding Domains ◽  
Phosphorylation Domain

Abstract In this investigation low, non-solubilizing concentrations of the strong anionic detergent SDS were used to perturbate the interaction of Ca2+ and Pi with their respective binding domains on the sarcoplasmic reticulum Ca-transport ATPase. Rising SDS concentrations produce a two-step decline of Ca2+-dependent ATP hydrolysis. At pH 6.15, SDS differently affects high affinity Ca2+ binding and phosphorylation by inorganic phosphate and releases the “mutual exclusion” of these two ligand binding steps. The degree of uncoupling is considerably more pronounced in the presence of 20% Me2SO. The reduction of Ca2+ binding by SDS is demonstrated to be a result of decreased affinity of one of the two specific high affinity binding sites and of perturbation of their cooperative interaction. Higher SDS partially restores the original high Ca2+ affinity but not the cooperativity of binding. Phosphorylation exhibits a higher SDS sensitivity than Ca2+ binding: Increasing SDS competitively inhibits and then completely abolishes phosphoenzyme formation. Thus. SDS binds to the phosphorylation domain, evidently involving the Lys352 residue of the ATPase molecule; this is accompanied by a more unspecific concentration-dependent SDS effect, probably mediated by hydrophobic force, which, finally, suppresses phosphorylation. Me2SO does neither qualitatively affect the SDS-dependent chemical properties of the vesicular material nor the SDS-dependent perturbation of the investigated reaction steps.

Sila-Pharmaka, 31. Mitt. [1] Synthese, Struktur und pharmakologische Eigenschaften von Diphenyl(2-piperidinoethoxymethyl)silanol und seinem Kohlenstoff-Analogon / Sila-Pharmaca, 31 th Communication [1] Synthesis, Structure, and Pharmacological Properties of Diphenyl(2-piperidinoethoxymethyl)silanol and its Carbon Analogue

1983 ◽  
Vol 38 (6) ◽  
pp. 738-746 ◽  
Author(s):  
Reinhold Tacke ◽  
Hartwig Lange ◽  
William S. Sheldrick ◽  
Günter Lambrecht ◽  
Ulrich Moser ◽  
...  
Keyword(s):  
Solid State ◽  
Hydrogen Bonds ◽  
Chemical Properties ◽  
Pharmacological Properties ◽  
Physical And Chemical Properties ◽  
Antimuscarinic Agents ◽  
Physical And Chemical ◽  
And Chemical Properties

Abstract In the course of systematic investigations on sila-substituted parasympatholytics the diphenyl(2-aminoethoxymethyl)silanols 3b and 4b (and its carbon analogue 4a) were synthesized and characterized by their physical and chemical properties. In the solid state 4a and 4b form strong O-H---N hydrogen bonds, which are intramolecular (4a) and intermolecular (4b), respectively. 4a and 4b were found to be weak antimuscarinic agents (4b >4a) and strong papaverine-like spasmolytics (4a ≈4b).

Molecular Cloning and Computational Analysis of Rice OsEm Gene

2014 ◽  
Vol 522-524 ◽  
pp. 1109-1116
Author(s):  
Jing Fan ◽  
Ming Yuan Huang ◽  
Xi Yu Zhang ◽  
Zi Liang ◽  
Cheng Hao Xu
Keyword(s):  
Phylogenetic Relationship ◽  
Protein Interaction ◽  
Protein Interaction Network ◽  
Chemical Properties ◽  
Alpha Helix ◽  
Interaction Network ◽  
Late Embryogenesis Abundant ◽  
Random Coil ◽  
Protein Protein Interaction ◽  
Protein Protein Interaction Network

Late embryogenesis abundant (LEA) proteins play important roles in enhancing the resistance of plants to adverse stresses and promoting seeds development and maturation. TheOsEmgene in rice is one of LEA protein-encoding genes, however, physical and chemical properties, phylogenetic relationship and protein-protein interaction network of it are still unknown. Here, the full length cDNA ofOsEmwas cloned using nested RT-PCR, the sequencing result was then computational analyzed using bioinformatics approaches. The results showed thatOsEmencoded a high hydrophilic protein with small molecule weight, it is mainly composed of alpha helix, extended strand, beta turn, random coil and contains a conserved region with 20 amino acid residues. Phylogenetic analysis showed that OsEM protein has the nearest phylogenetic relationship to BiEM1, but has the distant phylogenetic relationship to BnEM6. Results of protein-protein interaction network showed the expression ofOsEmgene was regulated by complexes ofVP1/BZ8orVP1/TRAB1. This work is helpful to further define the function ofOsEmgene and provide useful information for improving the adverse stress tolerance of plants in the future.

scholarly journals Hydrogen bonds and salt bridges across protein-protein interfaces

1997 ◽  
Vol 10 (9) ◽  
pp. 999-1012 ◽  
Author(s):  
D. Xu ◽  
C. J. Tsai ◽  
R. Nussinov
Keyword(s):  
Hydrogen Bonds ◽  
Salt Bridges ◽  
Protein Interfaces

Knowledge-based model of hydrogen-bonding propensity in organic crystals

2007 ◽  
Vol 63 (5) ◽  
pp. 768-782 ◽  
Author(s):  
Peter T. A. Galek ◽  
László Fábián ◽  
W. D. Samuel Motherwell ◽  
Frank H. Allen ◽  
Neil Feeder
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Three Dimensional ◽  
Chemical Properties ◽  
Organic Crystal ◽  
Training Data ◽  
Survey Method ◽  
Statistical Validation ◽  
Knowledge Based

A new method is presented to predict which donors and acceptors form hydrogen bonds in a crystal structure, based on the statistical analysis of hydrogen bonds in the Cambridge Structural Database (CSD). The method is named the logit hydrogen-bonding propensity (LHP) model. The approach has a potential application in identifying both likely and unusual hydrogen bonding, which can help to rationalize stable and metastable crystalline forms, of relevance to drug development in the pharmaceutical industry. Whilst polymorph prediction techniques are widely used, the LHP model is knowledge-based and is not restricted by the computational issues of polymorph prediction, and as such may form a valuable precursor to polymorph screening. Model construction applies logistic regression, using training data obtained with a new survey method based on the CSD system. The survey categorizes the hydrogen bonds and extracts model parameter values using descriptive structural and chemical properties from three-dimensional organic crystal structures. LHP predictions from a fitted model are made using two-dimensional observables alone. In the initial cases analysed, the model is highly accurate, achieving ∼ 90% correct classification of both observed hydrogen bonds and non-interacting donor–acceptor pairs. Extensive statistical validation shows the LHP model to be robust across a range of small-molecule organic crystal structures.

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