Palladium in the Chemical Synthesis and Modification of Proteins

The field of site‐specific modification of proteins has drawn significant attention in recent years owing to its importance in various research areas such as the development of novel therapeutics and understanding the biochemical and cellular behaviors of proteins. The presence of a large number of reactive functional groups in the protein of interest and in the cellular environment renders modification at a specific site a highly challenging task. With the development of sophisticated chemical methodologies it is now possible to target a specific site of a protein with a desired modification, however, many challenges remain to be solved. In this context, transition metals in particular palladium‐mediated C−C bond‐forming and C−O bond‐cleavage reactions gained great interest owing to the unique catalytic properties of palladium. Palladium chemistry is being explored for protein modifications in vitro, on the cell surface, and within the cell. Very recently, palladium complexes have been applied for the rapid deprotection of several widely utilized cysteine protecting groups as well as in the removal of solubilizing tags to facilitate chemical protein synthesis. This Minireview highlights these advances and how the accumulated knowledge of palladium chemistry for small molecules is being impressively transferred to synthesis and modification of chemical proteins.     

One-pot synthesis of Claisen–Schmidt reaction through (E)-chalcone derivatives: Spectral studies in human serum albumin protein binding and molecular docking investigation

An efficient and environmentally benign one-pot multicomponent synthesis of E-chalcones was developed using a mild and reusable new boron nitride-sulphonic acid catalyst. The catalyst was prepared by activating the boron nitride surface with nitric acid, followed by a simple reaction with 3-mercaptopropyl trimethoxysilane. The catalyst was characterized and morphological properties were studied by Fourier transform infrared, X-ray diffraction, transmission electron spectroscopy, scanning electron microscopy, Brunauer–Emmett–Teller theory, and Raman spectroscopy techniques. The solid acid catalyst was recycled five times in a Claisen–Schmidt reaction to synthesize new chalcone derivatives, and X-ray crystallography was used to elucidate the structure of (E)-1-(anthracen-9-yl)-3-(2-(4-methylpiperazin-1-yl)quinolin-3-yl)prop-2-en-1-one. A fluorescence quench titration method was used to assess its binding ability with human serum albumin (HSA), while molecular docking was also performed to get a more detailed insight into their interaction at the binding site of HSA.     

Facile synthesis of Fmoc-protected phosphonate pSer mimetic and its application in assembling a substrate peptide of 14-3-3 ζ

Phosphatase-inert peptidomimetics containing phosphonate pSer analogue have been developed as valuable biological tools for probing and regulating pSer-dependent protein-protein interactions (PPIs) in cellular context. Herein, we report a facile and efficient synthesis route of Fmoc-protected phosphonate pSer mimetic and also present the application of this building block in the solid-phase synthesis of a phosphatase-resistant substrate peptide of 14-3-3 ζ, retaining 14-3-3 ζ binding efficacy similar to the parent pSer-containing peptide.     

Rapid and accurate assessment of GPCR–ligand interactions Using the fragment molecular orbital‐based density‐functional tight‐binding method

The reliable and precise evaluation of receptor–ligand interactions and pair‐interaction energy is an essential element of rational drug design. While quantum mechanical (QM) methods have been a promising means by which to achieve this, traditional QM is not applicable for large biological systems due to its high computational cost. Here, the fragment molecular orbital (FMO) method has been used to accelerate QM calculations, and by combining FMO with the density‐functional tight‐binding (DFTB) method we are able to decrease computational cost 1000 times, achieving results in seconds, instead of hours. We have applied FMO‐DFTB to three different GPCR–ligand systems. Our results correlate well with site directed mutagenesis data and findings presented in the published literature, demonstrating that FMO‐DFTB is a rapid and accurate means of GPCR–ligand interactions. © 2017 Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.     

Temperature‐shuffled parallel cascade selection molecular dynamics accelerates the structural transitions of proteins

Parallel cascade selection molecular dynamics (PaCS‐MD) is an enhanced conformational sampling method for searching structural transition pathways from a given reactant to a product. Recently, a temperature‐aided PaCS‐MD (Vinod et al., Eur. Biophys. J. 2016, 45, 463) has been proposed as its extension, in which the temperatures were introduced as additional parameters in conformational resampling, whereas the temperature is fixed in the original PaCS‐MD. In the present study, temperature‐shuffled PaCS‐MD is proposed as a further extension of temperature‐aided PaCS‐MD in which the temperatures are shuffled among different replicas at the beginning of each cycle of conformational resampling. To evaluate their conformational sampling efficiencies, the original, temperature‐aided, and temperature‐shuffled PaCS‐MD were applied to a protein‐folding process of Trp‐cage, and their minimum computational costs to identify the native state were addressed. Through the evaluation, it was confirmed that temperature‐shuffled PaCS‐MD remarkably accelerated the protein‐folding process of Trp‐cage compared with the other methods. © 2017 Wiley Periodicals, Inc.     

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.     

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.