Multivalent-Interaction-Driven Assembly of Discrete,Flexible, and Asymmetric Supramolecular Protein Nano-Prisms

Current approaches to design monodisperse protein assemblies require rigid, tight, and symmetric interactions between oligomeric protein units. Herein, we introduce a new multivalent-interaction-driven assembly strategy that allows flexible, spaced, and asymmetric assembly between protein oligomers. We discovered that two polygonal protein oligomers (ranging from triangle to hexagon) dominantly form a discrete and stable two-layered protein prism nanostructure via multivalent interactions between fused binding pairs. We demonstrated that protein nano-prisms with long flexible peptide linkers (over 80 amino acids) between protein oligomer layers could be discretely formed. Oligomers with different structures could also be monodispersely assembled into two-layered but asymmetric protein nano-prisms. Furthermore, producing higher-order architectures with multiple oligomer layers, for example, 3-layered nano-prisms or nanotubes, was also feasible.     

Detection of discriminative sequence motifs in proteins obtained from prokaryotes grown at various temperatures

Recent investigations on the stability of proteins have demonstrated various structural factors, but few have considered sequence factors such as protein motifs. These motifs represent highly conserved regions and describe critical regions that may only exist on proteins that remain functional at high temperatures. This investigation presents a method for identifying and comparing corresponding mesophilic and thermophilic sequence motifs between protein families. Discriminative motifs that are conserved only in the mesophilic or thermophilic subfamily are identified. Analysis of the results shows that, although the subfamilies of most protein families share similar motifs, some discriminative motifs are present in particular thermophilic/mesophilic subfamilies. The thermophilic discriminative motifs are conserved only in thermophilic organisms, revealing that physiochemical principles support thermostability.     

An Off‐Pathway Folding Intermediate of an Acyl Carrier Protein Domain Coexists with the Folded and Unfolded States under Native Conditions

A protein can exist in multiple states under native conditions and those states with low populations are often critical to biological function and self‐assembly. To investigate the role of the minor states of an acyl carrier protein, NMR techniques were applied to determine the number of minor states and characterize their structures and kinetics. The acyl carrier protein from Micromonospora echinospora was found to exist in one major folded state (95.2 %), one unfolded state (4.1 %), and one intermediate state (0.7 %) under native conditions. The three states are in dynamic equilibrium and the intermediate state very likely adopts a native‐like structure and is an off‐pathway folding product. The intermediate state may mediate the formation of oligomers in vitro and play an important role in the recognition of partner enzymes in vivo.     

Chitin-binding antifungal protein from <Emphasis Type="Italic">Ficus carica</Emphasis> latex

A low-molecular-weight protein with antifungal activity was isolated from freshly collected latex of the Inzhir tree (Ficus carica L.) by successive affinity chromatography over chitin, cation-exchange chromatography over SP-Sephadex C-50, and reversed-phase HPLC. The molecular weight of 6481 and the partial N-terminus sequence of the protein were determined (MALDI-TOFMS). __________ Translated from Khimiya Prirodnykh Soedinenii, No. 2, pp. 171–173, March–April, 2008.     

Substitution of an Internal Disulfide Bridge with a Diselenide Enhances both Foldability and Stability of Human Insulin

Insulin analogues, mainstays in the modern treatment of diabetes mellitus, exemplify the utility of protein engineering in molecular pharmacology. Whereas chemical syntheses of the individual A and B chains were accomplished in the early 1960s, their combination to form native insulin remains inefficient because of competing disulfide pairing and aggregation. To overcome these limitations, we envisioned an alternative approach: pairwise substitution of cysteine residues with selenocysteine (Sec, U). To this end, Cys^A6 and Cys^A11 (which form the internal intrachain A6–A11 disulfide bridge) were each replaced with Sec. The A chain[C6U, C11U] variant was prepared by solid-phase peptide synthesis; while sulfitolysis of biosynthetic human insulin provided wild-type B chain-di-S-sulfonate. The presence of selenium atoms at these sites markedly enhanced the rate and fidelity of chain combination, thus solving a long-standing challenge in chemical insulin synthesis. The affinity of the Se-insulin analogue for the lectin-purified insulin receptor was indistinguishable from that of WT-insulin. Remarkably, the thermodynamic stability of the analogue at 25 °C, as inferred from guanidine denaturation studies, was augmented (ΔΔG_u ≈0.8 kcal mol⁻¹). In accordance with such enhanced stability, reductive unfolding of the Se-insulin analogue and resistance to enzymatic cleavage by Glu-C protease occurred four times more slowly than that of WT-insulin. 2D-NMR and X-ray crystallographic studies demonstrated a native-like three-dimensional structure in which the diselenide bridge was accommodated in the hydrophobic core without steric clash.     

SpyTag/SpyCatcher Cyclization Confers Resilience to Boiling on a Mesophilic Enzyme

SpyTag is a peptide that spontaneously forms an amide bond with its protein partner SpyCatcher. SpyTag was fused at the N terminus of β‐lactamase and SpyCatcher at the C terminus so that the partners could react to lock together the termini of the enzyme. The wild‐type enzyme aggregates above 37 °C, with irreversible loss of activity. Cyclized β‐lactamase was soluble even after heating at 100 °C; after cooling, the catalytic activity was restored. SpyTag/SpyCatcher cyclization led to a much larger increase in stability than that achieved through point mutation or alternative approaches to cyclization. Cyclized dihydrofolate reductase was similarly resilient. Analyzing unfolding through calorimetry indicated that cyclization did not increase the unfolding temperature but rather facilitated refolding after thermal stress. SpyTag/SpyCatcher sandwiching represents a simple and efficient route to enzyme cyclization, with potential to greatly enhance the robustness of biocatalysts.     

Screening the molecular surface of human anticoagulant protein C: A search for interaction sites

Protein C (PC), a 62 kDa multi-modular zymogen, is activated to an anticoagulant serine protease (activated PC or APC) by thrombin bound to thrombomodulin on the surface of endothelial cells. PC/APC interacts with many proteins and the characterisation of these interactions is not trivial. However, molecular modelling methods help to study these complex biological processes and provide basis for rational experimental design and interpretation of the results. PC/APC consists of a Gla domain followed by two EGF modules and a serine protease domain. In this report, we present two structural models for full-length APC and two equivalent models for full-length PC, based on the X-ray structures of Gla-domainless APC and of known serine protease zymogens. The overall elongated shape of the models is further cross-validated using size exclusion chromatography which allows evaluation of the Stokes radius (r_s for PC = 33.15 Å r_s for APC = 34.19 Å), frictional ratio and axial ratio. We then propose potential binding sites at the surface of PC/APC using surface hydrophobicity as a determinant of the preferred sites of intermolecular recognition. Most of the predicted binding sites are consistent with previously reported experimental data, while some clusters highlight new regions that should be involved in protein-protein interactions.     

Cellular Synthesis and X‐ray Crystal Structure of a Designed Protein Heterocatenane

Herein, we report the biosynthesis of protein heterocatenanes using a programmed sequence of multiple post‐translational processing events including intramolecular chain entanglement, in situ backbone cleavage, and spontaneous cyclization. The approach is general, autonomous, and can obviate the need for any additional enzymes. The catenane topology was convincingly proven using a combination of SDS‐PAGE, LC‐MS, size exclusion chromatography, controlled proteolytic digestion, and protein crystallography. The X‐ray crystal structure clearly shows two mechanically interlocked protein rings with intact folded domains. It opens new avenues in the nascent field of protein‐topology engineering.     

Cellular Synthesis and X-ray Crystal Structure of a Designed Protein Heterocatenane

Herein, we report the biosynthesis of protein heterocatenanes using a programmed sequence of multiple post-translational processing events including intramolecular chain entanglement, in situ backbone cleavage, and spontaneous cyclization. The approach is general, autonomous, and can obviate the need for any additional enzymes. The catenane topology was convincingly proven using a combination of SDS-PAGE, LC-MS, size exclusion chromatography, controlled proteolytic digestion, and protein crystallography. The X-ray crystal structure clearly shows two mechanically interlocked protein rings with intact folded domains. It opens new avenues in the nascent field of protein-topology engineering.     

蛋白质修饰的电化学研究

蛋白质的翻译后修饰对于生命体执行正常的生理功能具有十分重要的作用,是蛋白质科学研究的重要内容.目前研究蛋白质修饰的方法主要有质谱法、亲和层析等,然而由于蛋白质修饰研究的复杂性,迫切需要发掘新的技术手段.电化学方法理论成熟、应用广泛,在生命科学许多领域发挥着越来越重要的作用.蛋白质的体外修饰必将导致蛋白质特定位点基团的变化,可以利用巧妙设计的电化学方法予以表征和分析,以期探明修饰对蛋白质结构和功能的影响.此外,又可以利用电化学定量分析的独特优势快速准确地测定蛋白质修饰中涉及的相关酶活.正因为如此,蛋白质体外修饰的电化学研究已引起越来越多的关注.本文以作者课题组近期研究工作为主,结合国内外同行的相关代表性工作,介绍电化学方法在蛋白质修饰方面的近期研究进展,并探讨了今后的发展方向和趋势.     

Induced Folding of Protein‐Sized Foldameric β‐Sandwich Models with Core β‐Amino Acid Residues

The mimicry of protein‐sized β‐sheet structures with unnatural peptidic sequences (foldamers) is a considerable challenge. In this work, the de novo designed betabellin‐14 β‐sheet has been used as a template, and α→β residue mutations were carried out in the hydrophobic core (positions 12 and 19). β‐Residues with diverse structural properties were utilized: Homologous β³‐amino acids, (1R,2S)‐2‐aminocyclopentanecarboxylic acid (ACPC), (1R,2S)‐2‐aminocyclohexanecarboxylic acid (ACHC), (1R,2S)‐2‐aminocyclohex‐3‐enecarboxylic acid (ACEC), and (1S,2S,3R,5S)‐2‐amino‐6,6‐dimethylbicyclo[3.1.1]heptane‐3‐carboxylic acid (ABHC). Six α/β‐peptidic chains were constructed in both monomeric and disulfide‐linked dimeric forms. Structural studies based on circular dichroism spectroscopy, the analysis of NMR chemical shifts, and molecular dynamics simulations revealed that dimerization induced β‐sheet formation in the 64‐residue foldameric systems. Core replacement with (1R,2S)‐ACHC was found to be unique among the β‐amino acid building blocks studied because it was simultaneously able to maintain the interstrand hydrogen‐bonding network and to fit sterically into the hydrophobic interior of the β‐sandwich. The novel β‐sandwich model containing 25 % unnatural building blocks afforded protein‐like thermal denaturation behavior.     

Chemical Perturbation of Oncogenic Protein Folding: from the Prediction of Locally Unstable Structures to the Design of Disruptors of Hsp90–Client Interactions

Protein folding quality control in cells requires the activity of a class of proteins known as molecular chaperones. Heat shock protein-90 (Hsp90), a multidomain ATP driven molecular machine, is a prime representative of this family of proteins. Interactions between Hsp90, its co-chaperones, and client proteins have been shown to be important in facilitating the correct folding and activation of clients. Hsp90 levels and functions are elevated in tumor cells. Here, we computationally predict the regions on the native structures of clients c-Abl, c-Src, Cdk4, B-Raf and Glucocorticoid Receptor, that have the highest probability of undergoing local unfolding, despite being ordered in their native structures. Such regions represent potential ideal interaction points with the Hsp90-system. We synthesize mimics spanning these regions and confirm their interaction with partners of the Hsp90 complex (Hsp90, Cdc37 and Aha1) by Nuclear Magnetic Resonance (NMR). Designed mimics selectively disrupt the association of their respective clients with the Hsp90 machinery, leaving unrelated clients unperturbed and causing apoptosis in cancer cells. Overall, selective targeting of Hsp90 protein–protein interactions is achieved without causing indiscriminate degradation of all clients, setting the stage for the development of therapeutics based on specific chaperone:client perturbation.     

A Rapid Gas-Chromatography/Mass-Spectrometry Technique for Determining Odour Activity Values of Volatile Compounds in Plant Proteins: Soy,and Allergen-Free Pea and Brown Rice Protein

Plant-based protein sources have a characteristic aroma that limits their usage in various meat-alternative formulations. Despite being the most popular plant-based protein, the allergenicity of soy protein severely restricts the potential adoption of soy protein as an animal substitute. Thereby, allergen-free plant-protein sources need to be characterized. Herein, we demonstrate a rapid solid-phase-microextraction gas-chromatography/mass-spectrometry (SPME-GC/MS) technique for comparing the volatile aroma profile concentration of two different allergen-free plant-protein sources (brown rice and pea) and comparing them with soy protein. The extraction procedure consisted of making a 1:7 w/v aqueous plant protein slurry, and then absorbing the volatile compounds on an SPME fibre under agitation for 10 min at 40 °C, which was subsequently injected onto a GC column coupled to an MS system. Observed volatile concentrations were used in conjunction with odour threshold values to generate a Total Volatile Aroma Score for each protein sample. A total of 76 volatile compounds were identified. Aldehydes and furans were determined to be the most dominant volatiles present in the plant proteins. Both brown rice protein and pea protein contained 64% aldehydes and 18% furans, with minor contents of alcohols, ketones and other compounds. On the other hand, soy protein consisted of fewer aldehydes (46%), but a more significant proportion of furans (42%). However, in terms of total concentration, brown rice protein contained the highest intensity and number of volatile compounds. Based on the calculated odour activity values of the detected compounds, our study concludes that pea proteins could be used as a suitable alternative to soy proteins in applications for allergen-free vegan protein products without interfering with the taste or flavour of the product.     

Backbone building from quadrilaterals: a fast and accurate algorithm for protein backbone reconstruction from alpha carbon coordinates

In this contribution, we present an algorithm for protein backbone reconstruction that comprises very high computational efficiency with high accuracy. Reconstruction of the main chain atomic coordinates from the alpha carbon trace is a common task in protein modeling, including de novo structure prediction, comparative modeling, and processing experimental data. The method employed in this work follows the main idea of some earlier approaches to the problem. The details and careful design of the present approach are new and lead to the algorithm that outperforms all commonly used earlier applications. BBQ (Backbone Building from Quadrilaterals) program has been extensively tested both on native structures as well as on near-native decoy models and compared with the different available existing methods. Obtained results provide a comprehensive benchmark of existing tools and evaluate their applicability to a large scale modeling using a reduced representation of protein conformational space. The BBQ package is available for downloading from our website at http://biocomp.chem.uw.edu.pl/services/BBQ/. This webpage also provides a user manual that describes BBQ functions in detail.     

翻译后修饰Tau蛋白及其化学全/半合成

Tau蛋白是一种微管相关蛋白,有6种亚型,由352~441氨基酸组成。Tau蛋白的错误折叠和聚集与Tau蛋白病(Tauopathies),如阿尔茨海默病(AD)密切相关。目前在临床患者样本中可检测到具有各种翻译后修饰的Tau蛋白,这些翻译后修饰可能是AD发病机制的关键因素。本文综述了Tau蛋白常见的翻译后修饰,尤其是退行性疾病相关的翻译后修饰,以及化学全/半合成制备具有特定位点修饰、均一的Tau蛋白的进展。通过回顾翻译后修饰Tau蛋白的研究,可以更深入理解翻译后修饰对Tau蛋白的生理和病理作用,阐明翻译后修饰的调控机制,为相关疾病诊疗研究打下基础。     

A study of using luminophore-doped silica nanoparticles as fluorescent probe in protein microarray assay

A convenient method for the synthesis of tris(2,2′-bipyridyl) dichlororuthenium(II) hexahydrate-doped amino-modified double-layer silica nanoparticles is presented in this paper. The synthesized nanoparticles are uniform and photostable, and can be well dispersed in a water solution. Proteins could be directly immobilized onto these nanoparticles by a simple coupling process without losing their biological activities. These nanoparticles were further used as fluorescent probes in protein microarray assay for the quantitative detection of protein. The results obtained by these nanoparticles, with the detection limit of as low as 3.5 μg/mL, were much better than those involving the use of conventional FITC probe. Translated from Chinese Journal of Analytical Chemistry, 2006, 34(9): 1227–1230 (in Chinese)     

Electrophoresis of Native Proteins on Agarose Gels Containing Volatile Buffers

Abstract

Protein mixtures were resolved under non denaturing conditions on agarose gels containing the volatile buffer ammonium bicarbonate. Proteins were detected on a guide strip of the gel by a rapid staining method and the corresponding bands cut from the gel and eluted by centrifugation. The proteins were then obtained by lyophilization. Native proteins in the gel could be rapidly blotted onto nitrocellulose paper by capillary transfer.