Computational analysis for the determination of deleterious nsSNPs in human MTHFD1 gene

Single nucleotide polymorphisms (SNPs) are the most common genetic polymorphisms and play a major role in many inherited diseases. Methylenetetrahydrofolate dehydrogenase 1 (MTHFD1) is one of the enzymes involved in folate metabolism. In the present study, the functional and structural consequences of nsSNPs of human MTHFD1 gene was analyzed using various computational tools like SIFT, PolyPhen2, PANTHER, PROVEAN, SNAP2, nsSNPAnalyzer, PhD-SNP, SNPs&GO, I-Mutant, MuPro, ConSurf, InterPro, NCBI Conserved Domain Search tool, ModPred, SPARKS-X, RAMPAGE, FT Site and PyMol. Out of 327 nsSNPs form human MTHFD1 gene, total 45 SNPs were predicted as functionally most significant SNPs, among which 17 were highly conserved and functional, 17 were highly conserved and structural residues. Among 45 most significant SNPs, 15 were predicted to be involved in post translational modifications. The p.Gly165Arg may interfere in homodimer interface formation. The p.Asn439Lys and p.Asp445Asn may interfere in binding interactions of MTHFD1 protein with cesium cation and potassium. The two SNPs (p.Asp562Gly and p.Gly637Cys) might interfere in interactions of MTHFD1 with ligand.     

Protein C recognition by ion‐coordinated imprinted monolithic cryogels

The protein C imprinted monolithic cryogel was synthesized using 2‐hydroxyethyl methacrylate by redox cryo‐polymerization method. The prepared monolithic cryogel was characterized by Fourier transform infrared spectroscopy, swelling test, surface area measurements, and scanning electron microscopy. The nonimprinted cryogel was prepared as well for control. Adsorption of protein C from aqueous solutions was investigated in a continuous mode and several parameters affecting adsorption performance were optimized. The maximum protein C adsorption amount was 30.4 mg/g. The selectivity studies were performed by monolithic column studies and fast protein liquid chromatography, using hemoglobin and human serum albumin as competing proteins. The relative selectivity coefficients were 2.37 and 8.89 for hemoglobin and human serum albumin, respectively. Reusability was tested for ten consecutive adsorption–desorption cycles, and no significant change in adsorption capacity was recorded. A pseudo‐second‐order model was suitable to interpret kinetic data, and the Langmuir model suited the adsorption isotherms well.     

Electrospun Lipid Binding Proteins Composite Nanofibers with Antibacterial Properties

Electrospinning is here used for the first time to prepare nanofibers including a host/guest complex in a keratin/poly(ethylene oxide) matrix. The host is a lipid binding protein and the guest is an insoluble bactericidal molecule, irgasan, bound within the protein internal cavity. The obtained nanofibers, characterized by scanning electron microscopy, exhibit excellent antibacterial activity toward Gram positive and negative bacteria, even with a moderate protein/irgasan cargo. Solution NMR studies, employed to provide molecular information on the cargo system, points to a micromolar affinity, compatible with both the electrospinning process and slow guest release. The versatility of the carrier protein, capable of interacting with a variety of druggable hydrophobic molecules, is exploitable for the development of innovative biomedical devices, whose properties can be tuned by the selected guest.

     

Thin Poly(Di(Ethylene Glycol)Methyl Ether Methacrylate) Homopolymer Brushes Allow Controlled Adsorption and Desorption of PaTu 8988t Cells

Poly(di(ethylene glycol)methyl ether methacrylate) (PDEGMA) brushes, which are known to suppress protein adsorption and prevent cell attachment, are reported here to possess interesting and tunable thermoresponsive behavior, if the brush thickness is reduced or the grafting density is altered. PDEGMA brushes with a dry ellipsometric thickness of 5 ± 1 nm can be switched from cell adherent behavior at 37 °C to cell nonadherent at 25 °C. This behavior coincides with the temperature‐dependent irreversible adsorption of fibronectin from phosphate saline buffer and proteins present in the cell culture medium, as unveiled by surface plasmon resonance measurements. Unlike for tissue culture polystyrene reference surfaces, swelling of the PDEGMA chains below the lower critical solution temperature results in the absence of paxillin and actin containing cellular filaments responsible for cell attachment. These tunable properties of very thin homopolymer PDEGMA brushes render this system interesting as an alternative thermoresponsive layer for continuous cell culture or enzyme‐free cell culture systems.

     

Visible Laser‐Induced In Situ Cell Detachment from Gold Nanoparticle‐Embedded Collagen Gel

Cell sorting is important for cell biology and regenerative medicine. A visible light‐responsive cell scaffold is produced using gold nanoparticles and collagen gel. Various kinds of cells are cultured on the visible light‐responsive cell scaffold, and the target cells are selectively detached by photoirradiation without any cytotoxicity. This is a new image‐guided cell sorting system.

     

Highly Ordered Self‐Assembly of Native Proteins into 1D, 2D,and 3D Structures Modulated by the Tether Length of Assembly‐Inducing Ligands

In nature, proteins self‐assemble into various structures with different dimensions. To construct these nanostructures in laboratories, normally proteins with different symmetries are selected. However, most of these approaches are engineering‐intensive and highly dependent on the accuracy of the protein design. Herein, we report that a simple native protein LecA assembles into one‐dimensional nanoribbons and nanowires, two‐dimensional nanosheets, and three‐dimensional layered structures controlled mainly by small‐molecule assembly‐inducing ligands RnG (n =1, 2, 3, 4, 5) with varying numbers of ethylene oxide repeating units. To understand the formation mechanism of the different morphologies controlled by the small‐molecule structure, molecular simulations were performed from microscopic and mesoscopic view, which presented a clear relationship between the molecular structure of the ligands and the assembled patterns. These results introduce an easy strategy to control the assembly structure and dimension, which could shed light on controlled protein assembly.     

A Whole Proteome Inventory of Background Photocrosslinker Binding

Affinity‐based protein profiling (AfBPP) is a widely applied method for the target identification of bioactive molecules. Probes containing photocrosslinkers, such as benzophenones, diazirines, and aryl azides, irreversibly link the molecule of interest to its target protein upon irradiation with UV light. Despite their prevalent application, little is known about photocrosslinker‐specific off‐targets, affecting the reliability of results. Herein, we investigated background protein labeling by gel‐free quantitative proteomics. Characteristic off‐targets were identified for each photoreactive group and compiled in a comprehensive inventory. In a proof‐of‐principle study, H8 , a protein kinase A inhibitor, was equipped with a diazirine moiety. Application of this photoprobe revealed, by alignment with the diazirine background, unprecedented insight into its in situ proteome targets. Taken together, our findings guide the identification of biologically relevant binders in photoprobe experiments.     

活性导向的化学探针在氨基酸反应活性表征中的应用进展

原创药物的研制得益于蛋白质新靶标的发现,而新靶标的发现依赖于高可信度、高通量的药物-蛋白质相互作用分析方法。蛋白质作为生命功能的执行者,其表达量、空间定位与结构差异直接影响药效的发挥。目前,超过85%的蛋白质尚被认为是无法成药的,主要原因是缺少药物分子靶向的空腔以及相应的反应活性位点。因此,基于蛋白质组学层次实现对氨基酸反应活性位点的表征成为原创共价靶向药物设计的关键,也是克服难以成药靶标蛋白问题的关键。近年来,质谱技术的飞速发展极大地推动了基于蛋白质组学技术的药物-靶蛋白相互作用研究。其中基于活性的蛋白质组分析(ABPP)策略是利用活性位点导向的化学探针分子在复杂样品中实现功能状态酶和药物靶标等蛋白质的检测。基于化学探针的开发和质谱定量技术的发展,ABPP技术在氨基酸反应活性表征研究中展现出重要的应用潜力,将助力于药物新靶标的发现和药物先导化合物的开发。ABPP策略主要基于蛋白质的活性特征进行富集,活性探针作为ABPP策略的核心,近年来取得了飞速进展。该文回顾了ABPP策略的发展历程,重点介绍基于广谱活性探针的ABPP技术在多种氨基酸反应活性筛选领域的研究进展,并对其在药物靶点发现中...     

Evidence for Multiple Binding Modes in the Initial Contact Between SARS-CoV-2 Spike S1 Protein and Cell Surface Glycans**

Infection of host cells by SARS-CoV-2 begins with recognition by the virus S (spike) protein of cell surface heparan sulfate (HS), tethering the virus to the extracellular matrix environment, and causing the subunit S1-RBD to undergo a conformational change into the ‘open’ conformation. These two events promote the binding of S1-RBD to the angiotensin converting enzyme 2 (ACE2) receptor, a preliminary step toward viral-cell membrane fusion. Combining ligand-based NMR spectroscopy with molecular dynamics, oligosaccharide analogues were used to explore the interactions between S1-RBD of SARS CoV-2 and HS, revealing several low-specificity binding modes and previously unidentified potential sites for the binding of extended HS polysaccharide chains. The evidence for multiple binding modes also suggest that highly specific inhibitors will not be optimal against protein S but, rather, diverse HS-based structures, characterized by high affinity and including multi-valent compounds, may be required.