Mobile loop mutations in an archaeal inositol monophosphatase: modulating three-metal ion assisted catalysis and lithium inhibition

ResidueFinder: extracting individual residue mentions from protein literature

Background

The revolution in molecular biology has shown how protein function and structure are based on specific sequences of amino acids. Thus, an important feature in many papers is the mention of the significance of individual amino acids in the context of the entire sequence of the protein. MutationFinder is a widely used program for finding mentions of specific mutations in texts. We report on augmenting the positive attributes of MutationFinder with a more inclusive regular expression list to create ResidueFinder, which finds mentions of native amino acids as well as mutations. We also consider parameter options for both ResidueFinder and MutationFinder to explore trade-offs between precision, recall, and computational efficiency. We test our methods and software in full text as well as abstracts.

Results

We find there is much more variety of formats for mentioning residues in the entire text of papers than in abstracts alone. Failure to take these multiple formats into account results in many false negatives in the program. Since MutationFinder, like several other programs, was primarily tested on abstracts, we found it necessary to build an expanded regular expression list to achieve acceptable recall in full text searches. We also discovered a number of artifacts arising from PDF to text conversion, which we wrote elements in the regular expression library to address. Taking into account those factors resulted in high recall on randomly selected primary research articles. We also developed a streamlined regular expression (called “cut”) which enables a several hundredfold speedup in both MutationFinder and ResidueFinder with only a modest compromise of recall. All regular expressions were tested using expanded F-measure statistics, i.e., we compute F_β for various values of where the larger the value of β the more recall is weighted, the smaller the value of β the more precision is weighted.

Conclusions

ResidueFinder is a simple, effective, and efficient program for finding individual residue mentions in primary literature starting with text files, implemented in Python, and available in SourceForge.net. The most computationally efficient versions of ResidueFinder could enable creation and maintenance of a database of residue mentions encompassing all articles in PubMed.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13326-021-00243-3.

Transferable interactions of Li+ and Mg2+ ions in polarizable models

Therapeutic implications of Li⁺, in many cases, stem from its ability to inhibit certain Mg²⁺-dependent enzymes, where it interacts with or substitutes for Mg²⁺. The underlying details of its action are, however, unknown. Molecular simulations can provide insights, but their reliability depends on how well they describe relative interactions of Li⁺ and Mg²⁺ with water and other biochemical groups. Here, we explore, benchmark, and recommend improvements to two simulation approaches: the one that employs an all-atom polarizable molecular mechanics (MM) model and the other that uses a hybrid quantum and MM implementation of the quasi-chemical theory (QCT). The strength of the former is that it describes thermal motions explicitly and that of the latter is that it derives local contributions from electron densities. Reference data are taken from the experiment, and also obtained systematically from CCSD(T) theory, followed by a benchmarked vdW-inclusive density functional theory. We find that the QCT model predicts relative hydration energies and structures in agreement with the experiment and without the need for additional parameterization. This implies that accurate descriptions of local interactions are essential. Consistent with this observation, recalibration of local interactions in the MM model, which reduces errors from 10.0 kcal/mol to 1.4 kcal/mol, also fixes aqueous phase properties. Finally, we show that ion-ligand transferability errors in the MM model can be reduced significantly from 10.3 kcal/mol to 1.2 kcal/mol by correcting the ligand's polarization term and by introducing Lennard-Jones cross-terms. In general, this work sets up systematic approaches to evaluate and improve molecular models of ions binding to proteins.

Systems Biology Understanding of the Effects of Lithium on Cancer

Lithium has many widely varying biochemical and phenomenological effects, suggesting that a systems biology approach is required to understand its action. Multiple lines of evidence point to lithium as a significant factor in development of cancer, showing that understanding lithium action is of high importance. In this paper we undertake first steps toward a systems approach by analyzing mutual enrichment between the interactomes of lithium-sensitive enzymes and the pathways associated with cancer. This work integrates information from two important databases, STRING, and KEGG pathways. We find that for the majority of cancer pathways the mutual enrichment is statistically highly significant, reinforcing previous lines of evidence that lithium is an important influence on cancer.

From direct to indirect lithium targets: a comprehensive review of omics data

Metal ions are critical to a wide range of biological processes.

Membrane interaction and functional plasticity of inositol polyphosphate 5-phosphatases

In this issue of Structure, Trésaugues and colleagues determined the interaction of membrane-bound phosphoinositides with three clinically significant human inositol polyphosphate 5-phosphatases (I5Ps). A comparison to the structures determined with soluble substrates revealed differences in the binding mode and suggested how the I5Ps and apurinic endonuclease (APE1) activities evolved from the same metal-binding active center.

Crystal structure of cbbF from Zymomonas mobilis and its functional implication

A phosphate group at the C1-atom of inositol-monophosphate (IMP) and fructose-1,6-bisphosphate (FBP) is hydrolyzed by a phosphatase IMPase and FBPase in a metal-dependent way, respectively. The two enzymes are almost indiscernible from each other because of their highly similar sequences and structures. Metal ions are bound to residues on the β1- and β2-strands and one mobile loop. However, FBP has another phosphate and FBPases exist as a higher oligomeric state, which may discriminate FBPases from IMPases. There are three genes annotated as FBPases in Zymomonas mobilis, termed also cbbF (ZmcbbF). The revealed crystal structure of one ZmcbbF shows a globular structure formed by five stacked layers. Twenty-five residues in the middle of the sequence form an α-helix and a β-strand, which occupy one side of the catalytic site. A non-polar Leu residue among them is protruded to the active site, pointing out unfavorable access of a bulky charged group to this side. In vitro assays have shown its dimeric form in solution. Interestingly, two β-strands of β1 and β2 are disordered in the ZmcbbF structure. These data indicate that ZmcbbF might structurally belong to IMPase, and imply that its active site would be reorganized in a yet unreported way.

Insights into the role of magnesium triad in myo-inositol monophosphatase: metal mechanism, substrate binding, and lithium therapy

myo-Inositol monophosphatase (IMPase) plays a pivotal role in the intracellular phosphatidylinositol cell signaling pathway. It has attracted considerable attention as a putative therapeutic target for lithium therapy in the treatment of bipolar disorder. A trio of activated cofactor Mg²⁺ ions is required for inositol monophosphate hydrolysis by IMPase. In the present study, computational studies, including two-layered ONIOM-based quantum mechanics/mechanical mechanics (QM/MM) calculations, molecular modeling, and molecular dynamics (MD) simulations, were performed to ascertain the role of the Mg²⁺ triad in the IMPase active site. The QM/MM calculations show that the structural identity of the nucleophilic water molecule W1 shared by Mg²⁺-1 and Mg²⁺-3, activated by Thr95/Asp47 dyad, is a hydroxide ion. Moreover, Mg²⁺-3 needs to be conjugated with Mg²⁺-1 in the binding site to create the activated nucleophilic hydroxide ion in accordance with the three-metal ion catalytic mechanism. The MD simulation of the IMPase-substrate-Mg²⁺ complex shows that the three Mg²⁺ ions promote substrate binding and help fix the phosphate moiety of the substrate for nucleophilic attack by the hydroxide ion. When Mg²⁺-2 is displaced with Li⁺, the MD simulations of the postreaction complex indicate that the conformation of the catalytic loop (residues 33 to 44) is disrupted and water molecule W2 does not coordinate with Li⁺. This disruption traps the inorganic phosphate and inositolate in the active site, which lead to IMPase inhibition. By contrast, in the native Mg²⁺ system, the W2 ligated by Mg²⁺-2 and Asp200 aids in protonation of the leaving inositolate moiety.

Cloning, overexpression, purification, crystallization and preliminary X-ray diffraction analysis of an inositol monophosphatase family protein (SAS2203) from Staphylococcus aureus MSSA476

The gene product of the sas2203 ORF of Staphylococcus aureus MSSA476 encodes a 30 kDa molecular-weight protein with a high sequence resemblance (29% identity) to tetrameric inositol monophosphatase from Thermotoga maritima. The protein was cloned, expressed, purified to homogeneity and crystallized. Crystals appeared in several conditions and good diffraction-quality crystals were obtained from 0.2 M Li(2)SO(4), 20% PEG 3350, 0.1 M HEPES pH 7.0 using the sitting-drop vapour-diffusion method. A complete diffraction data set was collected to 2.6 Å resolution using a Rigaku MicroMax-007 HF Cu Kα X-ray generator and a Rigaku R-AXIS IV(++) detector. The diffraction data were consistent with the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 49.98, b = 68.35, c = 143.79 Å, α = β = γ = 90°, and the crystal contained two molecules in the asymmetric unit.