MultiBac: from protein complex structures to synthetic viral nanosystems

The MultiBac baculovirus/insect cell expression vector system was conceived as a user-friendly, modular tool-kit for producing multiprotein complexes for structural biology applications. MultiBac has allowed the structure and function of many molecular machines to be elucidated, including previously inaccessible high-value drug targets. More recently, MultiBac developments have shifted to customized baculoviral genomes that are tailored for a range of applications, including synthesizing artificial proteins by genetic code expansion. We review some of these developments, including the ongoing rewiring of the MultiBac system for mammalian applications, notably CRISPR/Cas9-mediated gene editing.

Evaluation of β-Amyloid Peptides Fibrillation Induced by Nanomaterials Based on Molecular Dynamics and Surface Plasmon Resonance

This report investigated the effect of carbon nanomaterials, single-wall carbon nanotube (SWCNT) and graphene oxide, on fibrillation of β-amyloid 40 (Aβ40) based on surface plasmon resonance (SPR) and molecular dynamics (MD). MD simulations are carried out in order to reveal the molecular mechanisms of the interaction between nanomaterials and Aβ40. The strong interaction between Aβ40 and nanomaterials is related to Van der Waals forces and the Coulomb force, inducing delicate manipulation of the main bonding energy for fibrillation of Aβ40. The interaction energy between the Aβ peptide and graphene is higher than that of SWCNT. Experimental results show both carbon nanomaterials enhance the appearance of a critical nucleus for nucleation of peptide fibrils. Graphene is more beneficial to assist the nucleation process than SWCNT. Combination of SPR and molecular dynamics could be a high-throughput method to screen protein fibrillation.

Photocatalytic nanolithography of self-assembled monolayers and proteins

Self-assembled monolayers of alkylthiolates on gold and alkylsilanes on silicon dioxide have been patterned photocatalytically on sub-100 nm length-scales using both apertured near-field and apertureless methods. Apertured lithography was carried out by means of an argon ion laser (364 nm) coupled to cantilever-type near-field probes with a thin film of titania deposited over the aperture. Apertureless lithography was carried out with a helium-cadmium laser (325 nm) to excite titanium-coated, contact-mode atomic force microscope (AFM) probes. This latter approach is readily implementable on any commercial AFM system. Photodegradation occurred in both cases through the localized photocatalytic degradation of the monolayer. For alkanethiols, degradation of one thiol exposed the bare substrate, enabling refunctionalization of the bare gold by a second, contrasting thiol. For alkylsilanes, degradation of the adsorbate molecule provided a facile means for protein patterning. Lines were written in a protein-resistant film formed by the adsorption of oligo(ethylene glycol)-functionalized trichlorosilanes on glass, leading to the formation of sub-100 nm adhesive, aldehyde-functionalized regions. These were derivatized with aminobutylnitrilotriacetic acid, and complexed with Ni(2+), enabling the binding of histidine-labeled green fluorescent protein, which yielded bright fluorescence from 70-nm-wide lines that could be imaged clearly in a confocal microscope.

Generation of peptide-MHC class I complexes through UV-mediated ligand exchange

Major histocompatibility complex (MHC) class I molecules present peptide ligands on the cell surface for recognition by appropriate cytotoxic T cells. MHC-bound peptides are critical for the stability of the MHC complex, and standard strategies for the production of recombinant MHC complexes are based on in vitro refolding reactions with specific peptides. This strategy is not amenable to high-throughput production of vast collections of MHC molecules. We have developed conditional MHC ligands that form stable complexes with MHC molecules but can be cleaved upon UV irradiation. The resulting empty, peptide-receptive MHC molecules can be charged with epitopes of choice under native conditions. Here we describe in-depth procedures for the high-throughput production of peptide-MHC (pMHC) complexes by MHC exchange, the analysis of peptide exchange efficiency by ELISA and the parallel production of MHC tetramers for T-cell detection. The production of the conditional pMHC complex by an in vitro refolding reaction can be achieved within 2 weeks, and the actual high-throughput MHC peptide exchange and subsequent MHC tetramer formation require less than a day.

Phased Fiber Growth in a Peptide Conjugate: Aggregation and Disaggregation Studies

A glycine-rich, short pentapeptide conjugate 6, derived from the highly conserved copper-binding octarepeat region of the prion protein, exhibits a tendency to self-aggregate in a time-dependent fashion. Aging of 6 afforded an insight into the phased growth of spherical prefibrillar structures to fibers of long persistence length, as observed by a combination of microscopic techniques. Interestingly, growth of these fibers was inhibited by colchicine, a known inhibitor of microtubule polymerization in a concentration dependent fashion. This study offers an intriguing insight into the occurrence of prefibrillar intermediates on the path to the formation of full length peptide fibers. It is also envisaged that constructs such as 6 may also serve as simple models to study chemical intervention of protein aggregation.

Artificial metalloenzymes for enantioselective catalysis based on the noncovalent incorporation of organometallic moieties in a host protein

Enzymatic and homogeneous catalysis offer complementary means to produce enantiopure products. Incorporation of achiral, biotinylated aminodiphosphine-rhodium complexes in (strept)avidin affords enantioselective hydrogenation catalysts. A combined chemogenetic procedure allows the optimization of the activity and the selectivity of such artificial metalloenzymes: the reduction of acetamidoacrylate proceeds to produce N-acetamidoalanine in either 96 % ee (R) or 80 % ee (S). In addition to providing a chiral second coordination sphere and, thus, selectivity to the catalyst, the phenomenon of protein-accelerated catalysis (e.g., increased activity) was unraveled. Such artificial metalloenzymes based on the biotin-avidin technology display features that are reminiscent of both homogeneous and of enzymatic catalysis.

Preparation of nano-sized particles from collagen II by a high-voltage electrostatic field system

The pilot study describes a novel method for preparing nano-sized particles from collagen II using a high-voltage electrostatic field system. Observations from transmission electron microscopy showed that, in one of the cases, the nano-sized collagen II particles exhibited good sphericity, and the particles were in the range of 23.3+/-1.7 nm in diameter at the experimental setting of 3 kV cm(-1), for a 3 h treatment period and at 25 degrees C (with a collagen concentration of 0.2 mg ml(-1)). When the treatment temperature increased to 30 degrees C, the collagen II began to lose the tendency to form individually separated spherically shaped nano-particles. Moreover, a fibrous structure of collagen II was formed instead of a nano-particle shape at the temperature of 37 degrees C. This result is probably contributed to by an entropy-driven process that is termed fibrillogenesis, a larger force causing the collagen molecules to self-assemble and then form collagen fibrils. It is interesting to note that this is practically the first attempt to produce nano-particles directly from collagen II solution under the treatment of a high-voltage electrostatic field, together with a set of working parameters for the collagen concentration and low-temperature setting.

Amyloid formation of a protein in the absence of initial unfolding and destabilization of the native state

In 5% (v/v) trifluoroethanol, pH 5.5, 25 degrees C one of the acylphosphatases from Drosophila melanogaster (AcPDro2) forms fibrillar aggregates that bind thioflavin T and Congo red and have an extensive beta-sheet structure, as revealed by circular dichroism. Atomic force microscopy indicates that the fibrils and their constituent protofilaments have diameters compatible with those of natural amyloid fibrils. Spectroscopic and biochemical investigation, carried out using near- and far-UV circular dichroism, intrinsic and 1-anilino-8-naphthalenesulfonic acid-derived fluorescence, dynamic light scattering, and enzymatic activity assays, shows that AcPDro2 has, before aggregation, a secondary structure content packing around aromatic and hydrophobic residues, hydrodynamic diameter, and catalytic activity indistinguishable from those of the native protein. The native protein was found to have the same conformational stability under native and aggregating conditions, as determined from urea-induced unfolding. The kinetic analysis supports models in which AcPDro2 aggregates initially without need to unfold and subsequently undergoes a conformational change into amyloid-like structures. Although fully or partially unfolded states have a higher propensity to aggregate, the residual aggregation potential that proteins maintain upon complete folding can be physiologically relevant and be directly involved in the pathogenesis of some protein deposition diseases.

Amyloid fibril formation can proceed from different conformations of a partially unfolded protein

Protein misfolding and aggregation are interconnected processes involved in a wide variety of nonneuropathic, systemic, and neurodegenerative diseases. More generally, if mutations in sequence or changes in environmental conditions lead to partial unfolding of the native state of a protein, it will often aggregate, sometimes into well-defined fibrillar structures. A great deal of interest has been directed at discovering the characteristic features of metastable partially unfolded states that precede the aggregated states of proteins. In this work, human muscle acylphosphatase (AcP) has been first destabilized, by addition of urea or by means of elevated temperatures, and then incubated in the presence of different concentrations of 2,2,2, trifluoroethanol ranging from 5% to 25% (v/v). The results show that AcP is able to form both fibrillar and nonfibrillar aggregates with a high beta-sheet content from partially unfolded states with very different structural features. Moreover, the presence of alpha-helical structure in such a state does not appear to be a fundamental determinant of the ability to aggregate. The lack of ready aggregation under some of the conditions examined here is attributable primarily to the intrinsic properties of the solutions rather than to specific structural features of the partially unfolded states that precede aggregation. Aggregation appears to be favored when the solution conditions promote stable intermolecular interactions, particularly hydrogen bonds. In addition, the structures of the resulting aggregates are largely independent of the conformational properties of their soluble precursors.

An improved method for the solution cyclization of peptides under pseudo-high dilution conditions

Depending on the ring size, the cyclization of peptides often is accompanied by dimerization or cyclodimerization. Hence, these macrocyclizations have to be performed under high dilution conditions. Efficient cyclization of peptides in solution with a minimum amount of solvent succeeds, when a dual syringe pump is used to simultaneously add the linear peptide precursor and a coupling reagent from two separate syringes.

Equilibrium unfolding of an oligomeric protein involves formation of a multimeric intermediate state(s)

Superoxide dismutases (SODs) are important metalloenzymes which protect cells against oxidative stress by scavenging reactive superoxides. Missense mutations in SODs are known to lead to some familial cases of amyotrophic lateral sclerosis and several forms of cancers. In the present study, we investigate the guanidinium hydrochloride (GdnHCl)-induced equilibrium unfolding of apo-manganese superoxide dismutase (apo-MnSOD) isolated from Vibrio alginolyticus using a variety of biophysical techniques. GdnHCl-induced equilibrium unfolding of apo-MnSOD is non-cooperative and involves the accumulation of stable intermediate state(s). Results of 1-anilino-8-naphthalene sulfonate binding experiments suggest that the equilibrium intermediate state(s) accumulates maximally in 1.5M GdnHCl. The intermediate state(s) appears to be obligatory and occurs both in the unfolding and refolding pathways. Size-exclusion chromatography and sedimentation velocity data reveal that the equilibrium intermediate state(s) is multimeric. To our knowledge, this is the first report of the identification of a multimeric intermediate in the unfolding pathway(s) of oligomeric proteins. The formation and dissociation of the multimeric intermediate state(s) appears to dictate the fate of the protein either to refold to its native conformation or misfold and form aggregates as observed in amyotrophic lateral sclerosis.

Synthesis of peptide bioconjugates

Bioconjugates play an important role in several fields of biomolecular and biomedicinal sciences. Protein/polypeptide-based conjugates with covalently attached epitope peptides are considered as potential synthetic vaccine candidates and/or target antigens in affinity-based bioassays. This chapter describes the synthesis of two- and three-component bioconjugates using water-soluble branched chain polymeric polypeptides with multiple amino and/or carboxyl groups as macromolecular partners and oligopeptides as epitopes with small molecular mass. The synthetic procedures outline three major strategies for the incorporation of multiple copies of uniformly oriented peptide epitopes. In the first example, chloroacetylated polypeptide is conjugated with SH-peptide to form a thioether linkage. Second, two independent oligopeptides are introduced into a macromolecule by amide and disulfide bonds, respectively. In the third example, a new procedure is reported for the formation of disulfide bridges by the use of Npys-modified polypeptide and SH-peptide.