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

Craft, John W.; Legge, Glen B.

doi:10.1007/s10858-005-1199-0

Cited by 63 publications

(68 citation statements)

References 15 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Force field parameters for phosphoserine were obtained from Ref. 45. Residues missing in the crystal structures due to disorder were rebuilt using the ModLoop interface to Modeler (46).…”

Section: Methodsmentioning

confidence: 99%

Dual Function of Phosphoubiquitin in E3 Activation of Parkin

Walinda

Morimoto

Sugase

et al. 2016

Journal of Biological Chemistry

View full text Add to dashboard Cite

Mutations in the gene encoding parkin, an auto-inhibited E3 ubiquitin ligase that functions in the clearance of damaged mitochondria, are the most common cause of autosomal recessive juvenile Parkinsonism. The mechanism regulating parkin activation remains poorly understood. Here we show, by using isothermal titration calorimetry, solution NMR, and fluorescence spectroscopy, that parkin can bind ubiquitin and phosphomimetic ubiquitin by recognizing the canonical hydrophobic patch and C terminus of ubiquitin. The affinity of parkin for both phosphomimetic and unmodified ubiquitin is markedly enhanced upon removal of the ubiquitin-like (UBL) domain of parkin. This suggests that the agonistic binding of ubiquitin to parkin in trans is counterbalanced by the antagonistic activity of the parkin UBL domain in cis. Intriguingly, UBL binding is enthalpy-driven, whereas ubiquitin binding is driven by an increase in the total entropy of the system. These thermody- Mutations in the PARK2 gene that encodes the protein parkin have been found to cause a familial form of Parkinson disease termed autosomal recessive juvenile parkinsonism (AR-JP) 2 (1-3). Parkin is an E3 ubiquitin ligase of the RBR family (Fig. 1A). RBR-type ubiquitin ligases function by first forming a covalent thioester intermediate between a key catalytic cysteine and the C terminus of ubiquitin, and then transferring the activated ubiquitin to their substrate (4). Under basal conditions, parkin resides in the cytosol (5, 6), and cytosolic parkin is thought to be catalytically inactive (5). Accordingly, recently reported crystal structures show parkin in an auto-inhibited conformation; both the interaction platform with the incoming E2 enzyme and the catalytic cysteine residue Cys 431 are occluded because of intramolecular interactions (Fig. 1B) (7-9). Autoregulation of E3 activity by the formation of such inhibitory interactions is a common feature of RBR ligases and has been previously described for the ubiquitin ligases HHARI and HOIP (4, 10, 11).Parkin functions in the ubiquitylation of mitochondrial proteins, an event that initiates the degradation of dysfunctional mitochondria by mitophagy (5, 6); this implies that the latent E3 ubiquitin ligase activity of parkin can be released in response to external factors. At least two events are required to release the latent E3 activity of parkin in cells. It has been shown that upon loss of the electrochemical potential across the inner mitochondrial membrane, the protein kinase PINK1, which is anchored on the outer mitochondrial membrane with the kinase domain facing the cytoplasm, phosphorylates parkin at residue Ser 65 of its UBL domain (12-14). Furthermore, it has been reported that PINK1 also phosphorylates ubiquitin, intriguingly at the homologous residue Ser 65 , which is conserved between ubiquitin and the UBL domain of parkin (15)(16)(17).How these two phosphorylation events act together to convert parkin from an inactive to a catalytically active state is not fully understood. Alone, the two events ar...

show abstract

“…Force field parameters for phosphoserine were obtained from Ref. 45. Residues missing in the crystal structures due to disorder were rebuilt using the ModLoop interface to Modeler (46).…”

Section: Methodsmentioning

confidence: 99%

Dual Function of Phosphoubiquitin in E3 Activation of Parkin

Walinda

Morimoto

Sugase

et al. 2016

Journal of Biological Chemistry

View full text Add to dashboard Cite

show abstract

“…The force-field parameters for the phosphorylated serine and threonine were taken from Ref. [42], in which a charge state of -2 was assigned to the phosphate groups. For comparison, similar simulations were conducted with force field charmm36 using GROMACS software [43][44][45][46][47][48].…”

Section: Methodsmentioning

confidence: 99%

Effects of phosphorylation on the intrinsic propensity of backbone conformations of serine/threonine

Gao

Zhang

et al. 2016

J Biol Phys

View full text Add to dashboard Cite

Each amino acid has its intrinsic propensity for certain local backbone conformations, which can be further modulated by the physicochemical environment and post-translational modifications. In this work, we study the effects of phosphorylation on the intrinsic propensity for different local backbone conformations of serine/threonine by molecular dynamics simulations. We showed that phosphorylation has very different effects on the intrinsic propensity for certain local backbone conformations for the serine and threonine. The phosphorylation of serine increases the propensity of forming polyproline II, whereas that of threonine has the opposite effect. Detailed analysis showed that such different responses to phosphorylation mainly arise from their different perturbations to the backbone hydration and the geometrical constraints by forming sidechain-backbone hydrogen bonds due to phosphorylation. Such an effect of phosphorylation on backbone conformations can be crucial for understanding the molecular mechanism of phosphorylation-regulated protein structures/dynamics and functions.

show abstract

“…For PNAs parameterization we used the Sanders et al force field for PNA [46] downloaded from the RESP and ESP charge database (R.E.DD.B. http://q4md-forcefieldtools.org/REDDB Project ID = F93) [47], whereas the parameters for serine phosphate were taken from reference [48]. TIP3P water molecules were added with a minimum spacing of 10.0 Å from the box edges to the RNA:PNA molecules and Na + counterions were added to each system to reach the neutralization of the system.…”

Section: Methodsmentioning

confidence: 99%

Exploitation of a Very Small Peptide Nucleic Acid as a New Inhibitor of miR-509-3p Involved in the Regulation of Cystic Fibrosis Disease-Gene Expression

Amato

Tomaiuolo

Nici

et al. 2014

BioMed Research International

View full text Add to dashboard Cite

Computational techniques, and in particular molecular dynamics (MD) simulations, have been successfully used as a complementary technique to predict and analyse the structural behaviour of nucleic acids, including peptide nucleic acid- (PNA-) RNA hybrids. This study shows that a 7-base long PNA complementary to the seed region of miR-509-3p, one of the miRNAs involved in the posttranscriptional regulation of the CFTR disease-gene of Cystic Fibrosis, and bearing suitable functionalization at its N- and C-ends aimed at improving its resistance to nucleases and cellular uptake, is able to revert the expression of the luciferase gene containing the 3′UTR of the gene in A549 human lung cancer cells, in agreement with the MD results that pointed at the formation of a stable RNA/PNA heteroduplex notwithstanding the short sequence of the latter. The here reported results widen the interest towards the use of small PNAs as effective anti-miRNA agents.

show abstract

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

Cited by 63 publications

References 15 publications

Dual Function of Phosphoubiquitin in E3 Activation of Parkin

Dual Function of Phosphoubiquitin in E3 Activation of Parkin

Effects of phosphorylation on the intrinsic propensity of backbone conformations of serine/threonine

Exploitation of a Very Small Peptide Nucleic Acid as a New Inhibitor of miR-509-3p Involved in the Regulation of Cystic Fibrosis Disease-Gene Expression

Contact Info

Product

Resources

About