Integration of A Deep Learning Classifier with A Random Forest Approach for Predicting Malonylation Sites

As a newly-identified protein post-translational modification, malonylation is involved in a variety of biological functions. Recognizing malonylation sites in substrates represents an initial but crucial step in elucidating the molecular mechanisms underlying protein malonylation. In this study, we constructed a deep learning(DL) network classifier based on long short-term memory(LSTM) with word embedding(LSTMWE) for the prediction of mammalian malonylation sites.LSTMWEperforms better than traditional classifiers developed with common pre-defined feature encodings or a DL classifier based on LSTM with a one-hot vector. The performance of LSTMWE is sensitive to the size of the training set, but this limitation can be overcome by integration with a traditional machine learning(ML) classifier. Accordingly, an integrated approach called LEMP was developed, which includes LSTMWEand the random forest classifier with a novel encoding of enhanced amino acid content. LEMP performs not only better than the individual classifiers but also superior to the currently-available malonylation predictors. Additionally, it demonstrates a promising performance with a low false positive rate, which is highly useful in the prediction application. Overall, LEMP is a useful tool for easily identifying malonylation sites with high confidence.LEMP is available at http://www.bioinfogo.org/lemp.

The Dependence of <i>N</i>-Malonyltryptophan Formation in Plants on Water Deficit (Review)

Drought stress in plants is accompanied by several metabolic changes. One of them is the appearance of N-malonyltryptophan (MT) during leaf wilting of many species, but there is a significant number of plant species in which the appearance of MT did not occur. Plants of some species were able to synthesize also N-acetyltryptophan (AT). Excised tomato leaves incubated with D-amino acids (including D-Trp) transform them into malonyl- and acetyl-derivatives even without water deficit. However, MT which appeared during water deficit has been shown to contain L-Trp. Amino acid—1-amino-cyclopropane-1-carboxylic acid (ACC) is also malonylated during water deficit, but other L-amino acids were not malonylated. N-malonyl transferases specific for Trp and ACC have been found in several plants. The existence of N-malonyltransferase specific to L-Trp and appeared during water deficit in plants forming MT is supposed, but clear experimental proof has not been obtained yet. Plants can transform MT applied exogenously into Trp and further to indole-3-acetic acid (IAA). But no evidence has been appeared up to now that endogenous MT may be a source of IAA. It is unknown till now why it is necessary for plants of many species to malonylate only Trp during water deficit. How MT metabolized in animals and if it affects them is also unknown. The necessity to use molecular-genetic approaches for the elucidation of the physiological significance of MT formation during water deficit is underlined.

Irpexoates A-D,Four Triterpenoids with Malonyl Modifications from the Fruiting Bodies of the Medicinal Fungus Irpex lacteus

Four eburicane-type triterpenoids with malonyl modifications,namely irpexoates A-D(1-4),were isolated from the fruiting bodies of the medicinal fungus Irpex lacteus.The structures of the new compounds were established by extensive spectroscopic methods,including 1D and 2D NMR,HRESIMS spectroscopic analysis.Irpexoate B(2)displayed weak cytotoxicity against four human cancer cell lines(A-549,SMMC-7721,MCF-7,SW480)with IC50 values varying from 22.9 to 34.0 pM,and irpexoate D(4)showed weak cytotoxicity against the human cancer cell line SW480 with an IC50 value of 35.2μM.

Molecular characterization and structure basis of a malonyltransferase with both substrate promiscuity and catalytic regiospecificity from Cistanche tubulosa

Enzymatic malonylation of natural glycosides provides a promising alternative method for drug-like malonylated glycosides supply.However,the catalytic potential and structural basis of plant malonyltransferase are far from being fully elucidated.This work identified a new malonyltransferase CtMaT1 from Cistanche tubulosa.It displayed unprecedented mono-and/or di-malonylation activity toward diverse glucosides with different aglycons.A“one-pot”system by CtMaT1 and a malonyl-CoA synthetase was established to biosynthesize nine new malonylated glucosides.Structural investigations revealed that CtMaT1 possesses an adequately spacious acyl-acceptor pocket capable of accommodating diverse glucosides.Additionally,it recognizes malonyl-CoA through strong electrotactic and hydrogen interactions.QM/MM calculation revealed the H167-mediated SN2 reaction mechanism of CtMaT1,while dynamic simulations detected the formation of stable hydrogen bonds between the glucose-6-OH group and H167,resulting in its high malonylation regiospecificity.Calculated energy profiles of two isomeric glycosides highlighted lower reaction energy barriers towards glucoside substrates,emphasizing CtMaT1's preference for glucosides.Furthermore,a mutant CtMaT1H36A with notably increased di-malonylation activity was obtained.The underlying molecular mechanism was illuminated through MM/GBSA binding free energy calculation.This study significantly advances the understanding of plant acyltransferases from both functional and protein structural perspectives,while also providing a versatile tool for enzymatic malonylation applications in pharmacology.