In Silico Evidence That Protein Unfolding is a Precursor of Protein Aggregation

We present a computational study on the folding and aggregation of proteins in an aqueous environment, as a function of its concentration. We show how the increase of the concentration of individual protein species can induce a partial unfolding of the native conformation without the occurrence of aggregates. A further increment of the protein concentration results in the complete loss of the folded structures and induces the formation of protein aggregates. We discuss the effect of the protein interface on the water fluctuations in the protein hydration shell and their relevance in the protein-protein interaction.     

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.     

Organic Ligand Binding by a Hydrophobic Cavity in a Designed Tetrameric Coiled‐Coil Protein

The design and characterization of a hydrophobic cavity in de novo designed proteins provides a wide range of information about the functions of de novo proteins. We designed a de novo tetrameric coiled‐coil protein with a hydrophobic pocketlike cavity. Tetrameric coiled coils with hydrophobic cavities have previously been reported. By replacing one Leu residue at the a position with Ala, hydrophobic cavities that did not flatten out due to loose peptide chains were reliably created. To perform a detailed examination of the ligand‐binding characteristics of the cavities, we originally designed two other coiled‐coil proteins: AM2, with eight Ala substitutions at the adjacent a and d positions at the center of a bundled structure, and AM2W, with one Trp and seven Ala substitutions at the same positions. To increase the association of the helical peptides, each helical peptide was connected with flexible linkers, which resulted in a single peptide chain. These proteins exhibited CD spectra corresponding to superhelical structures, despite weakened hydrophobic packing. AM2W exhibited binding affinity for size‐complementary organic compounds. The dissociation constants, K_d, of AM2W were 220 nM for adamantane, 81 μM for 1‐adamantanol, and 294 μM for 1‐adamantaneacetic acid, as measured by fluorescence titration analyses. Although it was contrary to expectations, AM2 did not exhibit any binding affinity, probably due to structural defects around the designed hydrophobic cavity. Interestingly, AM2W exhibited incremental structure stability through ligand binding. Plugging of structural defects with organic ligands would be expected to facilitate protein folding.     

The Potential of a Protein Model Synthesized Absent of Methionine

Methionine is an amino acid long thought to be essential, but only in the case of protein synthesis initiation. In more recent years, methionine has been found to play an important role in antioxidant defense, stability, and modulation of cell and protein activity. Though these findings have expanded the previously held sentiment of methionine having a singular purpose within cells and proteins, the essential nature of methionine can still be challenged. Many of the features that give methionine its newfound functions are shared by the other sulfur-containing amino acid: cysteine. While the antioxidant, stabilizing, and cell/protein modulatory functions of cysteine have already been well established, recent findings have shown a similar hydrophobicity to methionine which suggests cysteine may be able to replace methionine in all functions outside of protein synthesis initiation with little effect on cell and protein function. Furthermore, a number of novel mechanisms for alternative initiation of protein synthesis have been identified that suggest a potential to bypass the traditional methionine-dependent initiation during times of stress. In this review, these findings are discussed with a number of examples that demonstrate a potential model for synthesizing a protein in the absence of methionine.     

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.     

Protein adsorption on a nanoparticle with a nanostructured surface

In the present study, the adsorption of a protein on a nanoparticle with a nanostructured surface, which is created using successively patterned Gaussian pillars (GPs), is simulated by considering the charge regulation within the electrical double layer of a silica nanoparticle (NP). Namely, the mathematical models for the adsorption mechanism, such as classical Langmuir model, extended Langmuir model, and two-state model, are coupled with charge regulation model. By this means, size and pH variables are able to included to the calculations. Moreover, free space, surface curvature, and conformational changes are also taken into account. For systematic investigation, the solution's pH, surface charge density, initial protein concentration, electrostatic charge of the protein, and the diameter of the spherical NP are varied. As a result, the vital properties of a nanoparticle, such as protonation/deprotonation, polarization, topography, and morphology, are considered in the current simulations. The surface charge density and surface chemistry change with NP and GP sizes. The present results reveal that the protein adsorption on an NP with a smooth surface reaches a faster complete surface coverage than an NP with a nanostructured surface. Both states of conformational changes are also affected by the presence of the GP.     

Towards a Quantitative Understanding of Protein Hydration and Volumetric Properties

Herein, we probe by pressure perturbation calorimetry (PPC) the coefficient of thermal expansion, the volumetric and the hydration properties of variants of a hyperstable variant of staphylococcal nuclease (SNase), Δ+PHS. The temperature‐dependent volumetric properties of the folded and unfolded states of the wild‐type protein are calculated with previously published data. The present PPC results are used to interpret the volume diagram and expansivity at a molecular level. We conclude that the expansivity of the unfolded state is, to a first approximation, temperature independent, while that of the folded state decreases with increasing temperature. Our data suggest that at low temperature the defining contribution to ΔV comes mainly from excluded volume differences and ΔV for unfolding is negative. In contrast, at high temperatures, differential solvation due to the increased exposed surface area of the unfolded state and, in particular, its larger thermal volume linked to the increased conformational dynamics of the unfolded state ensemble takes over and ΔV for unfolding eventually becomes positive.     

Common Patterns in Chaperone Interactions with a Native Client Protein

Many molecular chaperones are promiscuous and interact with a wide range of unfolded, quasi‐native, and native client proteins. The mechanisms by which chaperones interact with the highly diverse structures of native clients thus remain puzzling. In this work, we investigate at the atomic level how three ATP‐independent chaperones interact with a β‐sheet‐rich protein, the Fyn SH3 domain. The results reveal that the chaperone Spy recognizes the locally frustrated surface of the client Fyn SH3 and that the interaction is transient and highly dynamic, leaving the chaperone‐interacting surface on Fyn SH3 solvent accessible. The two alternative molecular chaperones SurA and Skp recognize the same locally frustrated surface of the Fyn SH3 domain. These results indicate dynamic recognition of frustrated segments as a common mechanism underlying the chaperone–native client interaction, which also provides a basis for chaperone promiscuousness.     

蛋白质顺序测定的策略

近年来蛋白质顺序测定在自动化、微量化与策略方面都有显著的进展。用DNA顺序分析技术间接地测定蛋白质顺序的策略已被广泛地采用,它能加快但不能代替蛋白质的顺序测定。质谱技术测定蛋白质顺序的途径也有了可喜的突破。高效液相色谱分离肽技术的发展、限制性酶切及各种选择性的化学与酶的降解方法的出现,为蛋白质顺序测定提供了更多可选用的工具。     

Flow Injection Fluoroimmunoassay for Human Transferrin Using a Protein a Immunoreactor

Abstract

A protein A immunoreactor (immobilized protein A) incorporating flow injection technique was used for on-line fluoroimmunoassay of human transferrin. Antibody immobilized on protein A and antibody-antigen complex formation took place in phosphate buffered saline (PBS, PH 7.4). After washing off excess lucifer yellow VS labelled human transferrin, the antibody-antigen complex was eluted with acid buffer and detected. Experimental variables have been studied and the method has been used to determine the transferrin contents in human serum.     

Establishing a Klebsiella pneumoniae-Based Cell-Free Protein Synthesis System

Cell-free protein synthesis (CFPS) systems are emerging as powerful platforms for in vitro protein production, which leads to the development of new CFPS systems for different applications. To expand the current CFPS toolkit, here we develop a novel CFPS system derived from a chassis microorganism Klebsiella pneumoniae, an important industrial host for heterologous protein expression and the production of many useful chemicals. First, we engineered the K. pneumoniae strain by deleting a capsule formation-associated wzy gene. This capsule-deficient strain enabled easy collection of the cell biomass for preparing cell extracts. Then, we optimized the procedure of cell extract preparation and the reaction conditions for CFPS. Finally, the optimized CFPS system was able to synthesize a reporter protein (superfolder green fluorescent protein, sfGFP) with a maximum yield of 253 ± 15.79 μg/mL. Looking forward, our K. pneumoniae-based CFPS system will not only expand the toolkit for protein synthesis, but also provide a new platform for constructing in vitro metabolic pathways for the synthesis of high-value chemicals.     

Cellular Synthesis of Protein Catenanes

Direct cellular production of topologically complex proteins is of great interest both in supramolecular chemistry and protein engineering. We describe the first cellular synthesis of protein catenanes through the use of the p53 dimerization domain to guide the intertwining of two protein chains and SpyTag–SpyCatcher chemistry for efficient cyclization. The catenane topology was unambiguously proven by SDS‐PAGE, SEC, and partial digestion experiments and was shown to confer enhanced stability toward trypsin digestion relative to monomeric control mutants. The assembly–reaction synergy enabled by protein folding and genetically encoded protein chemistry offers a convenient yet powerful approach for creating mechanically interlocked, complex protein topologies in vivo.     

Carnoquinolines Target Copper Dyshomeostasis,Aberrant Protein–Protein Interactions,and Oxidative Stress

Metal dysregulation, oxidative stress, protein modification, and aggregation are factors strictly interrelated and associated with neurodegenerative pathologies. As such, all of these aspects represent valid targets to counteract neurodegeneration and, therefore, the development of metal-binding compounds with other properties to combat multifactorial disorders is definitely on the rise. Herein, the synthesis and in-depth analysis of the first hybrids of carnosine and 8-hydroxyquinoline, carnoquinolines (CarHQs), which combine the properties of the dipeptide with those of 8-hydroxyquinoline, are reported. CarHQs and their copper complexes were characterized through several techniques, such as ESI-MS and NMR, UV/Vis, and circular dichroism spectroscopy. CarHQs can modulate self- and copper-induced amyloid-β aggregation. These hybrids combine the antioxidant activity of their parent compounds. Therefore, they can simultaneously scavenge free radicals and reactive carbonyl species, thanks to the phenolic group and imidazole ring. These results indicate that CarHQs are promising multifunctional candidates for neurodegenerative disorders and they are worthy of further studies.     

Protein Allostery at Atomic Resolution

Protein allostery is a phenomenon involving the long range coupling between two distal sites in a protein. In order to elucidate allostery at atomic resoluion on the ligand-binding WW domain of the enzyme Pin1, multistate structures were calculated from exact nuclear Overhauser effect (eNOE). In its free form, the protein undergoes a microsecond exchange between two states, one of which is predisposed to interact with its parent catalytic domain. In presence of the positive allosteric ligand, the equilibrium between the two states is shifted towards domain–domain interaction, suggesting a population shift model. In contrast, the allostery-suppressing ligand decouples the side-chain arrangement at the inter-domain interface thereby reducing the inter-domain interaction. As such, this mechanism is an example of dynamic allostery. The presented distinct modes of action highlight the power of the interplay between dynamics and function in the biological activity of proteins.     

蛋白表面分子印迹技术

蛋白印迹材料在生物分离、生物传感和医用生物材料等领域具有很强的应用价值并受到广泛关注。尽管小分子印迹技术已经成功应用于很多领域,但蛋白分子印迹仍然是挑战性研究课题。本文总结了蛋白表面印迹技术领域的研究进展,根据不同的蛋白表面印迹材料,详细叙述了蛋白表面分子印迹薄膜、核壳微球、纳米线、凝胶微粒、单层膜等印迹材料的制备过程、印迹方法和选择识别性能,讨论了蛋白表面分子印迹方法的优缺点,阐明了蛋白分子印迹未来发展的方向。     

Protein sequence threading,the alignment problem,and a two-step strategy

Conventionally, protein structure prediction via “threading” relies on some nonoptimal method to align a protein sequence to each member of a library of known structures. We show how a score function (force field) can be modified so as to allow the direct application of a dynamic programming algorithm to the problem. This involves an approximation whose damage can be minimized by an optimization process during score function parameter determination. The method is compared to sequence to structure alignments using a more conventional pair-wise score function and the frozen approximation. The new method produces results comparable to the frozen approximation, but is faster and has fewer adjustable parameters. It is also free of memory of the template's original amino acid sequence, and does not suffer from a problem of nonconvergence, which can be shown to occur with the frozen approximation. Alignments generated by the simplified score function can then be ranked using a second score function with the approximations removed. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1455–1467, 1999     

Quantitative Packaging of Active Enzymes into a Protein Cage

Genetic fusion of cargo proteins to a positively supercharged variant of green fluorescent protein enables their quantitative encapsulation by engineered lumazine synthase capsids possessing a negatively charged lumenal surface. This simple tagging system provides a robust and versatile means of creating hierarchically ordered protein assemblies for use as nanoreactors. The generality of the encapsulation strategy and its effect on enzyme function were investigated with eight structurally and mechanistically distinct catalysts.     

Chemical Strategies for Generating Protein Biochips

Protein biochips are at the heart of many medical and bioanalytical applications. Increasing interest has been focused on surface activation and subsequent functionalization strategies for immobilizing these biomolecules. Different approaches using covalent and noncovalent chemistry are reviewed; particular emphasis is placed on the chemical specificity of protein attachment and on retention of protein function. Strategies for creating protein patterns (as opposed to protein arrays) are also outlined. An outlook on promising and challenging future directions for protein biochip research and applications is also offered.