Surface Engineering of Top7 to Facilitate Structure Determination

Top7 is a de novo designed protein whose amino acid sequence has no evolutional trace. Such a property makes Top7 a suitable scaffold for studying the pure nature of protein and protein engineering applications. To use Top7 as an engineering scaffold, we initially attempted structure determination and found that crystals of our construct, which lacked the terminal hexahistidine tag, showed weak diffraction in X-ray structure determination. Thus, we decided to introduce surface residue mutations to facilitate crystal structure determination. The resulting surface mutants, Top7sm1 and Top7sm2, crystallized easily and diffracted to the resolution around 1.7 Å. Despite the improved data, we could not finalize the structures due to high R values. Although we could not identify the origin of the high R values of the surface mutants, we found that all the structures shared common packing architecture with consecutive intermolecular β-sheet formation aligned in one direction. Thus, we mutated the intermolecular interface to disrupt the intermolecular β-sheet formation, expecting to form a new crystal packing. The resulting mutant, Top7sm2-I68R, formed new crystal packing interactions as intended and diffracted to the resolution of 1.4 Å. The surface mutations contributed to crystal packing and high resolution. We finalized the structure model with the R/Rfree values of 0.20/0.24. Top7sm2-I68R can be a useful model protein due to its convenient structure determination.

In Vitro Investigation of Binding Interactions between Albumin–Gliclazide Model and Typical Hypotensive Drugs

Type 2 diabetes management usually requires polytherapy, which increases the risk of drug-to-drug interactions. Among the multiple diabetes comorbidities, hypertension is the most prevalent. This study aimed to investigate the binding interactions between the model protein, bovine albumin, and the hypoglycemic agent gliclazide (GLICL) in the presence of typical hypotensive drugs: quinapril hydrochloride (QUI), valsartan (VAL), furosemide (FUR), amlodipine besylate (AML), and atenolol (ATN). Spectroscopic techniques (fluorescence quenching, circular dichroism) and thermodynamic experiments were employed. The binding of the gliclazide to the albumin molecule was affected by the presence of an additional drug ligand, which was reflected by the reduced binding constant of the BSA–DRUG–GLICL system. This may indicate a possible GLICL displacement and its enhanced pharmacological effect, as manifested in clinical practice. The analysis of the thermodynamic parameters indicated the spontaneity of the reaction and emphasized the role of hydrogen bonding and van der Waals forces in these interactions. The secondary structure of the BSA remained almost unaffected.

Enhanced model protein adsorption of nanoparticulate hydroxyapatite thin films on silk sericin and fibroin surfaces

Hydroxyapatite coated metallic implants favorably combine the required biocompatibility with the mechanical properties. As an alternative to the industrial coating method of plasma spraying with inherently potential deleterious effects, sol-gel methods have attracted much attention. In this study, the effects of intermediate silk fibroin and silk sericin layers on the protein adsorption capacity of hydroxyapatite films formed by a particulate sol-gel method were determined experimentally. The preparation of the layered silk protein/hydroxyapatite structures on glass substrates, and the effects of the underlying silk proteins on the topography of the hydroxyapatite coatings were described. The topography of the hydroxyapatite layer fabricated on the silk sericin was such that the hydroxyapatite particles were oriented forming an oriented crystalline surface. The model protein (bovine serum albumin) adsorption increased to 2.62 µg/cm2 on the latter surface as compared to 1.37 µg/cm2 of hydroxyapatite on glass without an intermediate silk sericin layer.

Genetic Encoding of A Nonhydrolyzable Phosphotyrosine Analog in Mammalian Cells

Protein tyrosine phosphorylation plays a critical role in signal transduction and the regulation of many cellular processes. It is of great significance to understand the underlying regulatory mechanism of particular tyrosine phosphorylation events. Here we report the genetic incorporation of a phosphotyrosine (pTyr) analog, p-carboxymethyl-L-phenylalanine (CMF), into proteins in mammalian cells. This nonhydrolyzable pTyr analog can facilitate biological studies by removing complications caused by the dynamic interconversion between the phosphorylated and non-phosphorylated isoforms of a protein. The developed methodology was demonstrated by using the human signal transducer and activator of transcription-1 (STAT1) as a model protein for homogeneous and defined incorporation of CMF. This tool will greatly enhance our capability to study protein tyrosine phosphorylation-associated biomolecular and cellular events, and enhance biomedical research that target protein tyrosine phosphorylation, which will have a broad impact to both fundamental studies and practical applications.

Emergence of planar cell polarity from the interplay of asymmetric interaction and tissue-level gradients

Planar cell polarity (PCP) - asymmetric localization of proteins at cell-cell interface - is essential for embryonic development and physiological functions. Abnormalities in PCP can lead to neural tube closure defects, misalignment in hair follicles etc. Thus, decoding the mechanism responsible for PCP establishment and maintenance remains an open fundamental question. While various molecules-broadly classified into 'global' and 'local' modules have been well investigated; their necessity and sufficiency in explaining PCP and connecting their perturbations and defects in experimentally observed patterns has not been examined. Here, we develop a minimal model that captures the proposed features of these two modules- a tissue level gradient (global) and asymmetric localization of protein complexes (local). Our model results suggest that while polarity can emerge in absence of a gradient; the gradient can provide the direction of polarity as well as offer robustness for maintenance of PCP in presence of stochastic perturbations. We also recapitulated swirling patterns (seen experimentally) and the features of non-domineering autonomy; using only three free parameters in the model - protein binding rate; concentration of proteins forming heterodimer across cell boundaries and steepness of gradient. Our results explain how self-stabilizing asymmetric localisations in presence of tissue-level gradient can lead to robust PCP patterns in diverse biological systems and reveals the minimal design principles for a polarized system.

Expanding the Scope of Polyoxometalates as Artificial Proteases towards Hydrolysis of Insoluble Proteins

Despite the enormous importance of insoluble proteins in biological processes, their structural investigation remains a challenging task. Development of artificial enzymatic catalysts would greatly facilitate elucidation of their structure as currently used enzymes in proteomics largely lose activity in the presence of surfactants, which are necessary to solubilize insoluble proteins. In this study the hydrolysis of a fully insoluble protein by a polyoxometalate complex as an artificial protease in surfactant solutions is reported for the first time. The hydrolysis of zein as a model protein was investigated in the presence of Zr(IV)-substituted Keggin-type polyoxometalate (POM), (Et2NH2)10[Zr(α-PW11O39)2], and different concentrations of the anionic surfactant sodium dodecyl sulfate (SDS). The selective hydrolysis of the protein upon incubation with the catalyst was observed, and the results indicate that hydrolytic selectivity and activity of the POM catalysts strongly depends on the concentration of surfactant. The molecular interactions between the POM catalyst and zein in the presence of SDS were explored using a combination of spectroscopic techniques which indicated competitive binding between POM and SDS towards the protein. The formation of micellar superstructures in tertiary POM/surfactant/protein solutions has been confirmed by electrical conductivity and Dynamic Light Scattering.

On the Applicability of Electrophoresis for Protein Quantification

Polyacrylamide gel electrophoresis is widely used for studying proteins and protein-containing objects. However, it is employed most frequently as a qualitative method rather than a quantitative one. This paper shows the feasibility of routine digital image acquisition and mathematical processing of electropherograms for protein quantification when using vertical gel electrophoresis and Chrom & Spec software. Both the well-studied model protein molecules (bovine serum albumin) and more complex real-world protein-based products (casein-containing isolate for sports nutrition), which were subjected to mechanical activation in a planetary ball mill to obtain samples characterized by different protein denaturation degrees, were used as study objects. Protein quantification in the mechanically activated samples was carried out. The degree of destruction of individual protein was shown to be higher compared to that of the protein-containing mixture after mechanical treatment for an identical amount of time. The methodological approach used in this study can serve as guidance for other researchers who would like to use electrophoresis for protein quantification both in individual form and in protein mixtures. The findings prove that photographic imaging of gels followed by mathematical data processing can be applied for analyzing the electrophoretic data as an affordable, convenient and quick tool.

Two energy barriers and a transient intermediate state determine the unfolding and folding dynamics of cold shock protein

Cold shock protein (Csp) is a typical two-state folding model protein which has been widely studied by biochemistry and single molecule techniques. Recently two-state property of Csp was confirmed by atomic force microscopy (AFM) through direct pulling measurement, while several long-lifetime intermediate states were found by force-clamp AFM. We systematically studied force-dependent folding and unfolding dynamics of Csp using magnetic tweezers with intrinsic constant force capability. Here we report that Csp mostly folds and unfolds with a single step over force range from 5 pN to 50 pN, and the unfolding rates show different force sensitivities at forces below and above ~8 pN, which determines a free energy landscape with two barriers and a transient intermediate state between them along one transition pathway. Our results provide a new insight on protein folding mechanism of two-state proteins.