Detecting the native ligand orientation by interfacial rigidity: SiteInterlock

Understanding the physical attributes of protein‐ligand interfaces, the source of most biological activity, is a fundamental problem in biophysics. Knowing the characteristic features of interfaces also enables the design of molecules with potent and selective interactions. Prediction of native protein‐ligand interactions has traditionally focused on the development of physics‐based potential energy functions, empirical scoring functions that are fit to binding data, and knowledge‐based potentials that assess the likelihood of pairwise interactions. Here we explore a new approach, testing the hypothesis that protein‐ligand binding results in computationally detectable rigidification of the protein‐ligand interface. Our SiteInterlock approach uses rigidity theory to efficiently measure the relative interfacial rigidity of a series of small‐molecule ligand orientations and conformations for a number of protein complexes. In the majority of cases, SiteInterlock detects a near‐native binding mode as being the most rigid, with particularly robust performance relative to other methods when the ligand‐free conformation of the protein is provided. The interfacial rigidification of both the protein and ligand prove to be important characteristics of the native binding mode. This measure of rigidity is also sensitive to the spatial coupling of interactions and bond‐rotational degrees of freedom in the interface. While the predictive performance of SiteInterlock is competitive with the best of the five other scoring functions tested, its measure of rigidity encompasses cooperative rather than just additive binding interactions, providing novel information for detecting native‐like complexes. SiteInterlock shows special strength in enhancing the prediction of native complexes by ruling out inaccurate poses. Proteins 2016; 84:1888–1901. © 2016 Wiley Periodicals, Inc.     

A simple innovative spectrofluorometric method for the determination of alendronate in bulk and in pharmaceutical tablets

Sodium alendronate is the first in a pharmacological class known as bisphosphonates, used for treatment of various bone diseases. Assay of bisphosphonates by a spectroscopic technique is very challenging due to the fact that they lack chromophores and none of them are fluorescent. In this work, a simple method is presented for determination of alendronate in bulk and in pharmaceutical tablets using spectrofluorometry by exploiting the ability of alendronate to displace salicylate from the iron(III)–salicylate chelate, forming a non‐fluorescent colorless iron(III)–alendronate complex. The liberated salicylate is fluorescent and is equivalent to the mount of alendronate added. The response was linear over the concentration range 20–90 μM and the proposed method was validated according to the guidelines of the International Conference on Harmonization. The correlation coefficient was found to be 0.995 and the limit of detection was 7.5 μM. The method was successfully applied for determination of alendronate in the commercially available Osteonate® tablets. The average percent recovery ± percent relative standard deviation was found to be 102.118 ± 2.033 which is congruent with the label claim of the dosage form. The results were also compared to a reported method using t‐test and F‐test at 95% confidence level; no significant differences were observed. The presented method is simple, fast, easy, cost‐effective and suitable for routine pharmaceutical analysis.     

The adduct formation between the thioguanine-polyamine ligands and DNA with the AP site under UVA irradiated and non-irradiated conditions

The AP sites are representative of DNA damage and known as an intermediate in the base excision repair (BER) pathway which is involved in the repair of damaged nucleobases by reactive oxygen species, UVA irradiation, and DNA alkylating agents. Therefore, it is expected that the inhibition or modulation of the AP site repair pathway may be a new type of anticancer drug. In this study, we investigated the effects of the thioguanine-polyamine ligands (^SG-ligands) on the affinity and the reactivity for the AP site under UVA irradiated and non-irradiated conditions. The ^SG-ligands have a photo-reactivity with the A-F-C sequence where F represents a tetrahydrofuran AP site analogue. Interestingly, the ^SG-ligands promoted the β-elimination of the AP site followed by the formation of a covalent bond with the β-eliminated fragment without UVA irradiation.     

High Conformational Variability in the GluK2 Kainate Receptor Ligand-Binding Domain

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EGFR配体生物学效应的多样性

表皮生长因子受体（epidermal growth factor receptor, EGFR）的配体作为一类重要的信号分子参与了细胞功能的调节,并且和机体发育、器官形成、组织修复与稳态维持,以及疾病的发生密切相关。虽然这些信号分子具有序列和结构上的相似性,但由于这些信号分子结构上的细微差异以及它们受体信号传导上的复杂性,造成了这些信号分子（配体）生物学效应的多样性。目前,从结构和机制上,对于单个信号分子的生物学效应已有较为深入的研究,但这些信号分子之间以及信号分子与受体之间的调控网络较为复杂,并且这种调控网络对信号的精细、有序和多样化转导至关重要。本文对EGFR配体的结构及配体生物学效应多样性的分子机制进行回顾,并对未来的研究方向提出展望。     

一种基于配体肽的CRP荧光检测探针的研制

C反应蛋白（C-reaction protein,CRP）是反映机体炎症的有效标志物,早期检测是判断炎症相关疾病的关键,因此,研制CRP新型检测制剂具有重要意义。利用噬菌体表面展示技术对CRP特异性亲和配体进行了筛选,采用固相肽合成技术对目标配体进行了合成,并经生物标记、高效液相色谱法（high performance liquid chromatography,HPLC）分析及质谱（mass spectrometry,MS）鉴定,成功制得检测CRP的荧光探针。经3轮筛选、ELISA检测、重组噬菌体测序及序列比对后得到1个目标配体肽：S-P-H-N-R-S-N-L-V-Q-E-L;经肽合成及生物标记获得1种CRP荧光探针：FITC-（Acp）-S-P-H-N-R-S-N-L-V-Q-E-L。研究结果为CRP的有效检测提供了一种新型制剂。     

Chemoattractant action and molecular signaling pathways of Kit ligand on mouse primordial germ cells

Using a Transwell chamber as migration assay for mouse primordial germ cells (PGCs), we show here that these cells posses directional migration in the absence of somatic cell and defined matrix support and in response to a Kit ligand (KL) gradient or medium conditioned by Aorta/Gonad/Mesonephros and gonadal ridges. Other putative PGC chemoattractants such as SDF1 and TGFbeta did not exert any attractive action on PGCs. The chemoattractant activity of KL and conditioned medium was also evidenced by their ability to stimulate actin reorganization in PGCs. In the aim to identify downstream signaling pathways governing KL chemoattraction on PGCs, we demonstrated that in such cells KL rapidly (5 min) increased autophosphorylation of its receptor c-Kit and caused phosphorylation of the serine-threonine kinase AKT through the action of PI3K. 740Y-P peptide, a direct activator of PI3 kinase, stimulated PGC migration at levels similar to those elicited by KL. LY294002 (a specific inhibitor of PI3K) abolished KL-dependent PGC migration or the chemoattractant activity of the conditioned medium and inhibited AKT phosphorylation; Src kinase inhibitors PP2 and SU6656, caused significant reduction of the KL-dependent PGC migration and AKT phosphorylation, while U0126, a selective inhibitor of the MEK/ERK protein kinase cascade, reduced PGC migration and AKT phosphorylation at lesser extent. SU6656 completely abolished the chemoattractant activity of the conditioned medium. Finally, SB202190 (a p38 inhibitor) and rapamycin (mTOR inhibitor) did not affect PGC migration. In addition, to demonstrate that somatic cells are not essential for PGC motility and directional migration, we evidenced a novel role for KL as PGC chemoattractant and for PI3K/AKT and Src kinase, as players involved in the activation of the PGC migratory machinery and likely important for their directional movement towards the gonadal ridges.     

The Cbl-interacting protein TULA inhibits dynamin-dependent endocytosis

The Cbl- and ubiquitin-interacting protein T-cell ubiquitin ligand (TULA) has been demonstrated to inhibit endocytosis and downregulation of ligand-activated EGF receptor (EGFR) by impairing Cbl-induced ubiquitination. We presently report that TULA additionally inhibited clathrin-dependent endocytosis in general, as both uptake of transferrin (Tf) and low-density lipoprotein (LDL) was inhibited. Additionally, endocytosis of the raft proteins CD59 and major histocompatibility complex class I (MHC-I), which we demonstrate were mainly endocytosed clathrin-independently, but dynamin-dependently, was blocked in cells overexpressing TULA. By contrast, the uptake of ricin, which is mainly endocytosed clathrin- and dynamin-independently, was not affected by overexpressed TULA. Consistently, TULA and dynamin co-immunoprecipitated and colocalized intracellularly, and upon overexpression of dynamin the TULA-mediated inhibitory effect on endocytosis of Tf, LDL, CD59 and MHC-I was counteracted. Overexpressed dynamin did not restore ubiquitination of the EGFR, and consistently dynamin did not rescue endocytosis of the EGFR in cells overexpressing TULA. We conclude that TULA inhibits both clathrin-dependent and clathrin-independent endocytic pathways by functionally sequestering dynamin via the SH3 domain of TULA binding proline-rich sequences in dynamin.     

OPA1 cleavage depends on decreased mitochondrial ATP level and bivalent metals

OPA1, an intra-mitochondrial dynamin GTPase, is a key actor of outer and inner mitochondrial membrane dynamic. OPA1 amino-terminal cleavage by PARL and m-AAA proteases was recently proposed to participate to the mitochondrial network dynamic in a DeltaPsi(m)-dependent way, and to apoptosis. Here, by an in vitro approach combining the use of purified mitochondrial fractions and mitochondrial targeting drugs, we intended to identify the central stimulus responsible for OPA1 cleavage. We confirm that apoptosis induction and PTPore opening, as well as DeltaPsi(m) dissipation induce OPA1 cleavage. Nevertheless, our experiments evidenced that decreased mitochondrial ATP levels, either generated by apoptosis induction, DeltaPsi(m) dissipation or inhibition of ATP synthase, is the common and crucial stimulus that controls OPA1 processing. In addition, we report that ectopic iron addition activates OPA1 cleavage, whereas zinc inhibits this process. These results suggest that the ATP-dependent OPA1 processing plays a central role in correlating the energetic metabolism to mitochondrial dynamic and might be involved in the pathophysiology of diseases associated to excess of iron or depletion of zinc and ATP.     

RAC3 down-regulation sensitizes human chronic myeloid leukemia cells to TRAIL-induced apoptosis

The nuclear receptor coactivator RAC3 plays important roles in many biological processes and tumorigenesis. We found that RAC3 is over-expressed in human chronic myeloid leukemia cells K562, which are normally resistant to TRAIL-induced apoptosis. RAC3 down-regulation by siRNA rendered these cells sensitive to TRAIL-induced cell death. In addition to the up-regulation of TRAIL receptors, the process involves Bid, caspases and PARP activation, loss of mitochondrial membrane potential, and release of AIF, cytochrome c and Smac/DIABLO to the cytoplasm. We conclude that RAC3 is required for TRAIL resistance and that this anti-apoptotic function is independent of its role in hormone receptor signaling.