Investigating Protein–Protein Allosteric Network using Current-Flow Scheme

Protein dynamic network analysis provides a powerful tool for investigating protein allosteric regulation. We recently developed a current-flow betweenness scheme for protein network analysis and demonstrated that this method, that is, using current-flow betweenness as edge weights, is more appropriate and more robust for investigating the signal transmission between two predefined protein residues or domains as compared with direct usage of correlation scores as edge weights. Here we seek to expand the current-flow scheme to study allosteric regulations involving protein–protein binding. Specifically, we investigated three gain-of-function mutations located at the binding interface of ALK2 (also known as ACVR1) kinase and its inhibitory protein FKBP12. We first searched for the optimal smoothing function for contact network construction and then calculated the subnetwork between FKBP12 protein and the kinase ATP binding site using current-flow betweenness. By comparing the networks between the wild-type and three mutants, we have identified statistically significant changes in the protein–protein networks that are common among all three mutants that allosterically shift the kinase toward a catalytically competent configuration. © 2019 Wiley Periodicals, Inc.     

Fragment-Based Stabilizers of Protein–Protein Interactions through Imine-Based Tethering

Small-molecule stabilization of protein–protein interactions (PPIs) is a promising concept in drug discovery, however the question how to identify or design chemical starting points in a “bottom-up” approach is largely unanswered. We report a novel concept for identifying initial chemical matter for PPI stabilization based on imine-forming fragments. The imine bond offers a covalent anchor for site-directed fragment targeting, whereas its transient nature enables efficient analysis of structure–activity relationships. This bond enables fragment identification and optimisation using protein crystallography. We report novel fragments that bind specifically to a lysine at the PPI interface of the p65-subunit-derived peptide of NF-κB with the adapter protein 14-3-3. Those fragments that subsequently establish contacts with the p65-derived peptide, rather than with 14-3-3, efficiently stabilize the 14-3-3/p65 complex and offer novel starting points for molecular glues.     

Quantifying Protein–Protein Interactions by Molecular Counting with Mass Photometry

Interactions between biomolecules control the processes of life in health and their malfunction in disease, making their characterization and quantification essential. Immobilization- and label-free analytical techniques are desirable because of their simplicity and minimal invasiveness, but they struggle with quantifying tight interactions. Here, we show that mass photometry can accurately count, distinguish by molecular mass, and thereby reveal the relative abundances of different unlabelled biomolecules and their complexes in mixtures at the single-molecule level. These measurements determine binding affinities over four orders of magnitude at equilibrium for both simple and complex stoichiometries within minutes, as well as the associated kinetics. These results introduce mass photometry as a rapid, simple and label-free method for studying sub-micromolar binding affinities, with potential for extension towards a universal approach for characterizing complex biomolecular interactions.     

Protein–Protein Binding Affinities in Solution Determined by Electrospray Mass Spectrometry

Electrospray ionization (ESI) allows the transfer of multi-protein complexes into the gas phase, thereby providing a simple approach for monitoring the stoichiometry of these noncovalent assemblies by mass spectrometry (MS). It remains unclear, however, whether the measured ion abundance ratios of free and bound species are suitable for determining solution-phase binding affinities (K _d values). Many types of mass spectrometers employ rf-only quadrupoles as ion guides. This work demonstrates that the settings used for these devices are a key factor for ensuring uniform transmission behavior, which is a prerequisite for meaningful affinity measurements. Using bovine β-lactoglobulin and hemoglobin as model systems, it is demonstrated that under carefully adjusted conditions the “direct” ESI-MS approach is capable of providing K _d values that are in good agreement with previously published solution-phase data. Of the several ion sources tested, a regular ESI emitter operated with pressure-driven flow at 1 μL min^–1 provided the most favorable results. Potential problems in these experiments include conformationally-induced differences in ionization efficiencies, inadvertent collision-induced dissociation, and ESI-induced clustering artifacts. A number of simple tests can be conducted to assess whether or not these factors are prevalent under the conditions used. In addition, the fidelity of the method can be scrutinized by performing measurements over a wide concentration range. Overall, this work supports the viability of the direct ESI-MS approach for determining binding affinities of protein–protein complexes in solution.     

Stable Isotope Labeling Strategy for Protein–Ligand Binding Analysis in Multi-Component Protein Mixtures

Described here is a stable isotope labeling protocol that can be used with a chemical modification- and mass spectrometry-based protein–ligand binding assay for detecting and quantifying both the direct and indirect binding events that result from protein–ligand binding interactions. The protocol utilizes an H₂¹⁶O₂ and H₂¹⁸O₂ labeling strategy to evaluate the chemical denaturant dependence of methionine oxidation in proteins both in the presence and absence of a target ligand. The differential denaturant dependence to the oxidation reactions performed in the presence and absence of ligand provides a measure of the protein stability changes that occur as a result of direct interactions of proteins with the target ligand and/or as a result of indirect interactions involving other protein–ligand interactions that are either induced or disrupted by the ligand. The described protocol utilizes the ¹⁸O/¹⁶O ratio in the oxidized protein samples to quantify the ligand-induced protein stability changes. The ratio is determined using the isotopic distributions observed for the methionine-containing peptides used for protein identification in the LC-MS-based proteomics readout. The strategy is applied to a multi-component protein mixture in this proof-of-principle experiment, which was designed to evaluate the technique’s ability to detect and quantify the direct binding interaction between cyclosporin A and cyclophilin A and to detect the indirect binding interaction between cyclosporin A and calcineurin (i.e., the protein–protein interaction between cyclophilin A and calcineurin that is induced by cyclosporin A binding to cyclophilin A).     

Selective Introduction of Sulfhydryl Groups into Recombinant Proteins for Study of Protein–Protein Interactions

In the present work, we proposed to create special sorbents for the study of protein–protein interactions, based on the fixation of cysteine-inserted beta-casein mutants with thiol-Sepharose resin. As a model system, we used bovine beta-casein, which belongs to the family of intrinsically unstructured proteins. Insertion of distal cysteines into the unfolded protein was not found to significantly change beta-casein properties. An amphiphilic beta-casein molecule has one hydrophilic domain and one hydrophobic domain placed on the N- and C-terminus, thus enabling one to exploit its capacity to engage in different types of intermolecular interactions. Two different casein-Sepharose sorbents incorporating either C-4 or C-208 beta-casein mutants bound to thiol-Sepharose were produced, exposing the hydrophobic domain in the case of the C-4 and the hydrophilic domain in the case of the C-208 mutant, respectively. The results obtained using the proposed sorbents with native beta-casein, another partially unfolded protein prion, and an oligomeric globular glyceraldehyde-3-phosphate dehydrogenase were found to be consistent with the data obtained by ELISA on free protein–protein complexes. Thus, Sepharose modified with various proteins is suitable for isolation of proteins interacting with the chromatographic phase bound partners from multicomponent systems such as milk. The obtained results allow the proposing of a fast and convenient method to be used for isolation of proteins, determination of protein-interacting partners, and the study of multi-protein complexes.

     

Selective Introduction of Sulfhydryl Groups into Recombinant Proteins for Study of Protein–Protein Interactions

In the present work, we proposed to create special sorbents for the study of protein–protein interactions, based on the fixation of cysteine-inserted beta-casein mutants with thiol-Sepharose resin. As a model system, we used bovine beta-casein, which belongs to the family of intrinsically unstructured proteins. Insertion of distal cysteines into the unfolded protein was not found to significantly change beta-casein properties. An amphiphilic beta-casein molecule has one hydrophilic domain and one hydrophobic domain placed on the N- and C-terminus, thus enabling one to exploit its capacity to engage in different types of intermolecular interactions. Two different casein-Sepharose sorbents incorporating either C-4 or C-208 beta-casein mutants bound to thiol-Sepharose were produced, exposing the hydrophobic domain in the case of the C-4 and the hydrophilic domain in the case of the C-208 mutant, respectively. The results obtained using the proposed sorbents with native beta-casein, another partially unfolded protein prion, and an oligomeric globular glyceraldehyde-3-phosphate dehydrogenase were found to be consistent with the data obtained by ELISA on free protein–protein complexes. Thus, Sepharose modified with various proteins is suitable for isolation of proteins interacting with the chromatographic phase bound partners from multicomponent systems such as milk. The obtained results allow the proposing of a fast and convenient method to be used for isolation of proteins, determination of protein-interacting partners, and the study of multi-protein complexes.     

A Bioorthogonal Click Chemistry Toolbox for Targeted Synthesis of Branched and Well-Defined Protein–Protein Conjugates

Bioorthogonal chemistry holds great potential to generate difficult-to-access protein–protein conjugate architectures. Current applications are hampered by challenging protein expression systems, slow conjugation chemistry, use of undesirable catalysts, or often do not result in quantitative product formation. Here we present a highly efficient technology for protein functionalization with commonly used bioorthogonal motifs for Diels–Alder cycloaddition with inverse electron demand (DA_inv). With the aim of precisely generating branched protein chimeras, we systematically assessed the reactivity, stability and side product formation of various bioorthogonal chemistries directly at the protein level. We demonstrate the efficiency and versatility of our conjugation platform using different functional proteins and the therapeutic antibody trastuzumab. This technology enables fast and routine access to tailored and hitherto inaccessible protein chimeras useful for a variety of scientific disciplines. We expect our work to substantially enhance antibody applications such as immunodetection and protein toxin-based targeted cancer therapies.     

Multicomponent Peptide Stapling as a Diversity-Driven Tool for the Development of Inhibitors of Protein–Protein Interactions

Stapled peptides are chemical entities in-between biologics and small molecules, which have proven to be the solution to high affinity protein–protein interaction antagonism, while keeping control over pharmacological performance such as stability and membrane penetration. We demonstrate that the multicomponent reaction-based stapling is an effective strategy for the development of α-helical peptides with highly potent dual antagonistic action of MDM2 and MDMX binding p53. Such a potent inhibitory activity of p53-MDM2/X interactions was assessed by fluorescence polarization, microscale thermophoresis, and 2D NMR, while several cocrystal structures with MDM2 were obtained. This MCR stapling protocol proved efficient and versatile in terms of diversity generation at the staple, as evidenced by the incorporation of both exo- and endo-cyclic hydrophobic moieties at the side chain cross-linkers. The interaction of the Ugi-staple fragments with the target protein was demonstrated by crystallography.     

Protein Data Bank中抗体的自动识别

我们发展了一种名为KIAb（Keyword-based Identification of Antibodies）的方法用于自动识别Protein Data Bank（PDB）中的抗体结构。该方法通过读取PDB格式的文件，查找与抗体相关的特定关键词并做出判断。我们使用该方法从PDB中识别出780个结构文件，经人工检查其中767个为抗体，成功率高达98.3%。结果基本包括了抗体结构数据库Summary of Antibody Crystal Structures（SACS）中收录的所有条目，而且还包括该数据库没有收录的34个抗体结构。因此该方法对PDB数据库中抗体的识别更为完备而且具有很低的假阳性率。     

Probing the Selectivity and Protein⋅Protein Interactions of a Nonreducing Fungal Polyketide Synthase Using Mechanism-Based Crosslinkers

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Delineating Protein–Protein Curvilinear Dissociation Pathways and Energetics with Naïve Multiple-Walker Umbrella Sampling Simulations

The protein–protein interaction energetics can be obtained by calculating the potential of mean force (PMF) from umbrella sampling (US) simulations, in which samplings are often enhanced along a predefined vector as the reaction coordinate. However, any slight change in the vector may significantly vary the calculated PMF, and therefore the energetics using a random choice of vector may mislead. A non-predefined curve path-based sampling enhancement approach is a natural alternative, but was relatively less explored for protein–protein systems. In this work, dissociation of the barnase–barstar complex is simulated by implementing non-predefined curvilinear pathways in US simulations. A simple variational principle is applied to determine the lower bound PMF, which could be used to derive the standard free energy of binding. Two major dissociation pathways, which include interactions with the RNA-binding loop and the Val 36 to Gly 40 loop, are observed. Further, the proposed approach was used to discriminate the decoys from protein–protein docking studies. © 2019 Wiley Periodicals, Inc.     

Protein—Protein Interactions in Aqueous Ammonium Sulfate Solutions. Lysozyme and Bovine Serum Albumin (BSA)

Osmotic pressures have been measured to determine lysozyme—lysozyme,BSA—BSA, and lysosyme—BSA interactions for protein concentrations to 100 g-L^–1in an aqueous solution of ammonium sulfate at ambient temperature, as a functionof ionic strength and pH. Osmotic second virial coefficients for lysozyme, forBSA, and for a mixture of BSA and lysozyme were calculated from theosmotic-pressure data for protein concentrations to 40 g-L^–1. The osmotic second virialcoefficient of lysozyme is slightly negative and becomes more negative withrising ionic strength and pH. The osmotic second virial coefficient for BSA isslightly positive, increasing with ionic strength and pH. The osmotic second virialcross coefficient of the mixture lies between the coefficients for lysozyme andBSA, indicating that the attractive forces for a lysozyme—BSA pair areintermediate between those for the lysozyme—lysozyme and BSA—BSA pairs. For proteinconcentrations less than 100 g-L^–1, experimental osmotic-pressure data comparefavorably with results from an adhesive hard-sphere model, which has previouslybeen shown to fit osmotic compressibilities of lysozyme solutions.     

A pH Switch for β-Sheet Protein Folding

Protein design advancements have led to biotechnological strategies based on more stable and more specific structures. Herein we present a 6-residue sequence (HPATGK) that acts as a stable structure-nucleating turn at physiological and higher pH but is notably unfavorable for chain direction reversal at low pH. When placed into the turn of a β-sheet, this leads to a pH switch of folding. Using a standard 3-stranded β-sheet model, the WW domain, it was found that the pH switch sequence insertion caused minimal change at pH 8 but a ca. 50 °C drop in the melting temperature (T_m) was observed at pH 2.5: ΔΔG_F ≥11.3 kJ mol⁻¹. Using the strategies demonstrated in this article, the redesign of β-sheets to contain a global, or local, pH-dependent conformational switch should be possible.     

Protein conformation in solution by three-dimensional fluorescence spectrometry

The conformations of bovine serum albumin (USA) and egg albumin (EA) in solution and their conformation changes under different conditions were studied by using three-dimensional fluorescence spectrometry (TDFS) such as three-dimensional fluorescence (TDF) spectra and three-dimensional fluorescence polarization (TDFP) spectra with tryptophan residues in protein molecules as an intrinsic fluorescent probe. The results show that the microenvironment of tryptophan residues of protein molecules in various solutions can be directly indicated and TDFS is an effective tool for studying protein conformation in solution. Meantime, some valuable results were obtained.     

Purification and Characterization of PRL Protein Tyrosine Phosphatases

PRLs constitute a subfamily of protein tyrosine phosphatases(PTPs). In the present paper are reported the molecular cloning, expression, purification, and characterization of all the three members of the PRL enzymes in human and the only PRL in C. elegans. These enzymes were expressed as glutathione S-transferase (GST) fusion proteins in DE3pLysS E. coil cells, and the recombinant fusion proteins were purified on glutathione-Sepharose affinity columns. Having been cleaved with thrombin, GST-free enzymes were further purified on an S-100 Sepharose gel filtration column. The purified proteins show single polypeptide bands on SDS-polyacrylamide gel electrophoresis. With para-nitrophenyl phosphate(p-NPP) as a substrate, PRLs exhibit classical Michaelis-Menten kinetics with Vmax values two orders of magnitude smaller than those of classic PTPs. The responses of PRLs to ionic strength, metal ions and phosphatase inhibitors are similar to those of other characterized PTPs, but their optimal pH values are different. These data thus reveal distinct common biochemical properties of PRL subfamily PTPs as well.     

Advances in Detection Methods of β-Amyloid Protein

Alzheimer's disease (AD) is a neurodegenerative disease with unknown etiology. β-amyloid protein (Aβ) is one of the specific biomarkers of AD, and many clinical studies suggest that abnormal levels of Aβ in blood, cerebrospinal fluid and brain tissue are closely related to the progression of AD. The analysis and evaluation of Aβ are important for early detection, tracking, prevention, and treatment of AD. In this paper, the present situations of the commonly used detection methods of Aβ at home and abroad were summarized and compared. Specifically, the latest application of new electrochemical biosensor in Aβ detection was mainly described, and the summary of its future directions and the potential applications was given.     

Automated Protein Structure Elucidation From 2D NMR

A general method for automated de novo deduction of protein structure from 2D NMR has been developed. The algorithms which extract simple spin coupling topologies from MQF-COSY, construct more complicated spin coupling topologies based upon MQ spectrum including all possible pathways, and extract spin coupling topological fragments for amino acids of a protein, have been implemented in C~(++) language and run on a SUN 4/280 work station. Compared with the manual assignments for melittin, the total identity of the automated de novo method is 86.3%.     

A Novel Protein Found in Selenium-rich Silkworm Pupas

Selenium(Se)is well known for its cancer-preventive function1.In our previous work,silkworm pupas from Ziyang county of Shanxi Province,one of the two largest Se-rich areas in China,was found to have Se content215times higher than that from Luoyang which is a normal region in China2.Meanwhile,Se-rich amino acids extracted from Ziyang pupas could efficiently induce the apoptosis of human hepatoma cells SMMC-7721.In order to find out the effective component responsible for this carcinostat…