Comparative study on activation mechanism of carboxypeptidase A1, A2 and B: first insights from steered molecular dynamics simulations

Structural Insights into the Catalytic Cycle of Inulin Fructotransferase: From Substrate Anchoring to Product Releasing

Carbohydrate degradation is crucial for living organisms due to their essential functions in providing energy and composing various metabolic pathways. Nevertheless, in the catalytic cycle of polysaccharide degradation, the details of how the substrates bind and how the products release need more case studies. Here, we choose an inulin fructotransferase (SpIFTase) as a model system, which can degrade inulin into functionally difructose anhydride I. At first, the crystal structures of SpIFTase in the absence of carbohydrates and complex with fructosyl-nystose (GF4), difructose anhydride I, and fructose are obtained, giving the substrate trajectory and product path of SpIFTase, which are further supported by steered molecular dynamics simulations (MDSs) along with mutagenesis. Furthermore, structural topology variations at the active centers of inulin fructotransferases are suggested as the structural base for product release, subsequently proven by substitution mutagenesis and MDSs. Therefore, this study provides a case in point for a deep understanding of the catalytic cycle with substrate trajectory and product path.

Structural analysis of TrkA mutations in patients with congenital insensitivity to pain reveals PLCγ as an analgesic drug target

Chronic pain is a major health issue, and the search for new analgesics has become increasingly important because of the addictive properties and unwanted side effects of opioids. To explore potentially new drug targets, we investigated mutations in the NTRK1 gene found in individuals with congenital insensitivity to pain with anhidrosis (CIPA). NTRK1 encodes tropomyosin receptor kinase A (TrkA), the receptor for nerve growth factor (NGF) and that contributes to nociception. Molecular modeling and biochemical analysis identified mutations that decreased the interaction between TrkA and one of its substrates and signaling effectors, phospholipase Cγ (PLCγ). We developed a cell-permeable phosphopeptide derived from TrkA (TAT-pQYP) that bound the Src homology domain 2 (SH2) of PLCγ. In HEK-293T cells, TAT-pQYP inhibited the binding of heterologously expressed TrkA to PLCγ and decreased NGF-induced, TrkA-mediated PLCγ activation and signaling. In mice, intraplantar administration of TAT-pQYP decreased mechanical sensitivity in an inflammatory pain model, suggesting that targeting this interaction may be analgesic. The findings demonstrate a strategy to identify new targets for pain relief by analyzing the signaling pathways that are perturbed in CIPA.

Why Should Metformin Not Be Given in Advanced Kidney Disease? Potential Leads from Computer Simulations

Metformin is considered as the go-to drug in the treatment of diabetes. However, it is either prescribed in lower doses or not prescribed at all to patients with kidney problems. To find a potential explanation for this practice, we employed atomistic-level computer simulations to simulate the transport of metformin through multidrug and toxin extrusion 1 (MATE1), a protein known to play a key role in the expulsion of metformin into urine. Herein, we examine the hydrogen bonding between MATE1 and one or more metformin molecules. The simulation results indicate that metformin continuously forms and breaks off hydrogen bonds with MATE1 residues. However, the mean hydrogen bond lifetimes increase for an order of magnitude when three metformin molecules are inserted instead of one. This new insight into the metformin transport process may provide the molecular foundation behind the clinical practice of not prescribing metformin to kidney disease patients.

Predicted gene 31453 (Gm31453) and the gene encoding carboxypeptidase A5 (Cpa5) are not essential for spermatogenesis and male fertility in the mouse

Numerous long non-coding (lnc) RNAs are highly enriched or exclusively expressed in the mammalian testis, even in spermatids. Spermatid perinuclear RNA-binding protein (STRBP) can bind many RNAs, and loss of STRBP impairs male fertility. However, the functions of lncRNAs interacting with STRBP are unknown. In this study, the roles of one STRBP-interacting lncRNA, namely predicted gene 31453 (Gm31453), and its potential target gene encoding carboxypeptidase A5 (Cpa5) in spermatogenesis were determined using gene-knockout (KO) mice. Gm31453 and Cpa5 are located adjacent to each other on the same chromosome and are highly expressed in the testis. Gm31453 and Cpa5 are primarily expressed from secondary spermatocytes to elongated spermatids, implying their involvement in spermiogenesis. Although deletion of Gm31453 disturbed the expression of both its target and interacting gene, as indicated by decreased Cpa5 and increased Strbp mRNA levels, both Gm31453- and Cpa5-KO mice showed normal spermatogenesis and fertility, and had no detectable abnormalities in terms of testicular and epididymal development, sperm production morphology or motility, pregnancy rate or litter size. Thus, Gm31453 and Cpa5 are dispensable for spermatogenesis and male fertility in mice. Their involvement in spermatogenesis may be a fine-tuning role, regulating gene expression at the molecular level.

A Novel Vasoactive Proline-Rich Oligopeptide from the Skin Secretion of the Frog Brachycephalus ephippium

Proline-rich oligopeptides (PROs) are a large family which comprises the bradykinin-potentiating peptides (BPPs). They inhibit the activity of the angiotensin I-converting enzyme (ACE) and have a typical pyroglutamyl (Pyr)/proline-rich structure at the N- and C-terminus, respectively. Furthermore, PROs decrease blood pressure in animals. In the present study, the isolation and biological characterization of a novel vasoactive BPP isolated from the skin secretion of the frog Brachycephalus ephippium is described. This new PRO, termed BPP-Brachy, has the primary structure WPPPKVSP and the amidated form termed BPP-BrachyNH₂ inhibits efficiently ACE in rat serum. In silico molecular modeling and docking studies suggest that BPP-BrachyNH₂ is capable of forming a hydrogen bond network as well as multiple van der Waals interactions with the rat ACE, which blocks the access of the substrate to the C-domain active site. Moreover, in rat thoracic aorta BPP-BrachyNH₂ induces potent endothelium-dependent vasodilatation with similar magnitude as captopril. In DAF-FM DA-loaded aortic cross sections examined by confocal microscopy, BPP-BrachyNH₂ was found to increase the release of nitric oxide (NO). Moreover, BPP-BrachyNH₂ was devoid of toxicity in endothelial and smooth muscle cell cultures. In conclusion, the peptide BPP-BrachyNH₂ has a novel sequence being the first BPP isolated from the skin secretion of the Brachycephalidae family. This opens for exploring amphibians as a source of new biomolecules. The BPP-BrachyNH₂ is devoid of cytotoxicity and elicits endothelium-dependent vasodilatation mediated by NO. These findings open for the possibility of potential application of these peptides in the treatment of endothelial dysfunction and cardiovascular diseases.

The unbinding studies of vascular endothelial growth factor receptor-2 protein tyrosine kinase type II inhibitors

Vascular endothelial growth factor receptor-2 (VEGFR-2) tyrosine kinase has two conformations, active and inactive conformations. Type II inhibitors bind to inactive conformation. It has two possible binding/unbinding paths. To explore the unbinding path of inhibitor 01-435 that was generated by fragment build in the binding pocket of VEGFR-2, molecular dynamics (MD) simulation was performed on the crystal structure of VEGFR-2 in complex with 01-435, then steered molecular dynamics (SMD) simulation was executed on the crystal structure of VEGFR-2 in complex with 01-435. Pull force, van der Waals and electrostatic interaction along the two paths were calculated by using SMD simulation. The SMD simulation results indicate that the more favorable path for inhibitor dissociation is along with the traditional ATP-channel rather than the allosteric-pocket-channel, which is mainly due to the less electrostatic interaction that the ligand suffers during dissociation process along the traditional ATP-channel.