Phosfinder: a web server for the identification of phosphate-binding sites on protein structures

Parca, Luca; Mangone, Iolanda; Gherardini, Pier Federico; Ausiello, Gabriele; Helmer-Citterich, Manuela

doi:10.1093/nar/gkr389

Cited by 12 publications

(9 citation statements)

References 30 publications

(34 reference statements)

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“…event that can be unambiguously assigned to the designed protein without concerns for contaminating activities. Binding of phosphate and phosphate-containing ligands is a widespread feature of modern proteins (43)(44)(45) and presumably one of the elementary functions that linked RNA and ribunucleoside cofactors to the earliest proteins (10,(46)(47)(48)(49)(50). Furthermore, during purification, it became apparent that the PLoop designs bind nucleic acids and interact with triphosphate and hexametaphosphate (SI Appendix, Fig.…”

Section: The Designed Ploop Proteins Bind Phosphorylated Nucleoside Lmentioning

confidence: 99%

Simple yet functional phosphate-loop proteins

Romero-Romero

Yang

Lin

et al. 2018

Proc. Natl. Acad. Sci. U.S.A.

129

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Abundant and essential motifs, such as phosphate-binding loops (P-loops), are presumed to be the seeds of modern enzymes. The Walker-A P-loop is absolutely essential in modern NTPase enzymes, in mediating binding, and transfer of the terminal phosphate groups of NTPs. However, NTPase function depends on many additional active-site residues placed throughout the protein’s scaffold. Can motifs such as P-loops confer function in a simpler context? We applied a phylogenetic analysis that yielded a sequence logo of the putative ancestral Walker-A P-loop element: a β-strand connected to an α-helix via the P-loop. Computational design incorporated this element into de novo designed β-α repeat proteins with relatively few sequence modifications. We obtained soluble, stable proteins that unlike modern P-loop NTPases bound ATP in a magnesium-independent manner. Foremost, these simple P-loop proteins avidly bound polynucleotides, RNA, and single-strand DNA, and mutations in the P-loop’s key residues abolished binding. Binding appears to be facilitated by the structural plasticity of these proteins, including quaternary structure polymorphism that promotes a combined action of multiple P-loops. Accordingly, oligomerization enabled a 55-aa protein carrying a single P-loop to confer avid polynucleotide binding. Overall, our results show that the P-loop Walker-A motif can be implemented in small and simple β-α repeat proteins, primarily as a polynucleotide binding motif.

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Section: The Designed Ploop Proteins Bind Phosphorylated Nucleoside Lmentioning

confidence: 99%

Simple yet functional phosphate-loop proteins

Romero-Romero

Yang

Lin

et al. 2018

Proc. Natl. Acad. Sci. U.S.A.

129

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“…In 53% of the analyzed proteins this method placed a correct nucleotide conformation in the first rank. We recently developed a method for the identification of phosphate binding sites, based on the identification of specific structural motifs [19], [20]. Here we extend this approach to the other nucleotide fragments.…”

Section: Introductionmentioning

confidence: 99%

Identification of Nucleotide-Binding Sites in Protein Structures: A Novel Approach Based on Nucleotide Modularity

et al. 2012

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Nucleotides are involved in several cellular processes, ranging from the transmission of genetic information, to energy transfer and storage. Both sequence and structure based methods have been developed to predict the location of nucleotide-binding sites in proteins. Here we propose a novel methodology that leverages the observation that nucleotide-binding sites have a modular structure. Nucleotides are composed of identifiable fragments, i.e. the phosphate, the nucleobase and the carbohydrate moieties. These fragments are bound by specific structural motifs that recur in proteins of different fold. Moreover these motifs behave as modules and are found in different combinations across fold space. Our method predicts binding sites for each nucleotide fragment by comparing a query protein with a database of templates extracted from proteins of known structure. Whenever a similarity is found the fragment bound by the template is transferred on the query protein, thus identifying a putative binding site. Predictions falling inside the surface of the protein are discarded, and the remaining ones are scored using clustering and conservation. The method is able to rank as first a correct prediction in the 48%, 48% and 68% of the analyzed proteins for the nucleobase, carbohydrate and phosphate respectively, while considering the first five predictions the performances change to 71%, 65% and 86% respectively. Furthermore we attempted to reconstruct the full structure of the binding site, starting from the predicted positions of the fragments. We calculated that in the 59% of the analyzed proteins the method ranks as first a reconstructed binding site or a part of it. Finally we tested the reliability of our method in a real world case in which it has to predict nucleotide-binding sites in unbound proteins. We analyzed proteins whose structure has been solved with and without the nucleotide and observed only little variations in the method performance.

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“…Two energy‐based approaches (Q‐SiteFinder4 and i‐Site20), a well‐established pocket identification program (LigSite21), a peptide‐binding site detection method (PepSite22), and a recent phospholigand‐binding site identification approach (Phosfinder23) were chosen for comparison against SiteHound (OP probe). Binding‐site identification coverage, defined as the percentage of known binding sites identified among the top three clusters with an MCC of at least 0.3, was used again as the measure of performance.…”

Section: Resultsmentioning

confidence: 99%

Automated identification of binding sites for phosphorylated ligands in protein structures

Ghersi

Sánchez

2012

Proteins

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Phosphorylation is a crucial step in many cellular processes, ranging from metabolic reactions involved in energy transformation to signaling cascades. In many instances, protein domains specifically recognize the phosphogroup. Knowledge of the binding site provides insights into the interaction, and it can also be exploited for therapeutic purposes. Previous studies have shown that proteins interacting with phosphogroups are highly heterogeneous, and no single property can be used to reliably identify the binding site. Here we present an energy-based computational procedure that exploits the protein 3D structure to identify binding sites involved in the recognition of phosphogroups. The procedure is validated on three datasets containing over 200 proteins binding to ATP, phosphopeptides, and phosphosugars. A comparison against other three generic binding site identification approaches shows higher accuracy values for our method, with a correct identification rate in the 80-90% range for the top three predicted sites. Addition of conservation information further improves the performance. The method presented here can be used as a first step in functional annotation, or to guide mutagenesis experiments and further studies such as molecular docking.

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Phosfinder: a web server for the identification of phosphate-binding sites on protein structures

Cited by 12 publications

References 30 publications

Simple yet functional phosphate-loop proteins

Simple yet functional phosphate-loop proteins

Identification of Nucleotide-Binding Sites in Protein Structures: A Novel Approach Based on Nucleotide Modularity

Automated identification of binding sites for phosphorylated ligands in protein structures

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