Turbidity as a useful optical parameter to predict protein crystallization by dynamic light scattering

Raman-based PAT for VLP precipitation: systematic data diversification and preprocessing pipeline identification

Virus-like particles (VLPs) are a promising class of biopharmaceuticals for vaccines and targeted delivery. Starting from clarified lysate, VLPs are typically captured by selective precipitation. While VLP precipitation is induced by step-wise or continuous precipitant addition, current monitoring approaches do not support the direct product quantification, and analytical methods usually require various, time-consuming processing and sample preparation steps. Here, the application of Raman spectroscopy combined with chemometric methods may allow the simultaneous quantification of the precipitated VLPs and precipitant owing to its demonstrated advantages in analyzing crude, complex mixtures. In this study, we present a Raman spectroscopy-based Process Analytical Technology (PAT) tool developed on batch and fed-batch precipitation experiments of Hepatitis B core Antigen VLPs. We conducted small-scale precipitation experiments providing a diversified data set with varying precipitation dynamics and backgrounds induced by initial dilution or spiking of clarified Escherichia coli-derived lysates. For the Raman spectroscopy data, various preprocessing operations were systematically combined allowing the identification of a preprocessing pipeline, which proved to effectively eliminate initial lysate composition variations as well as most interferences attributed to precipitates and the precipitant present in solution. The calibrated partial least squares models seamlessly predicted the precipitant concentration with R 2 of 0.98 and 0.97 in batch and fed-batch experiments, respectively, and captured the observed precipitation trends with R 2 of 0.74 and 0.64. Although the resolution of fine differences between experiments was limited due to the observed non-linear relationship between spectral data and the VLP concentration, this study provides a foundation for employing Raman spectroscopy as a PAT sensor for monitoring VLP precipitation processes with the potential to extend its applicability to other phase-behavior dependent processes or molecules.

Common Pitfalls and Recommendations for Using a Turbidity Assay to Study Protein Phase Separation

The turbidity assay is commonly exploited to study protein liquid-to-liquid phase separation (LLPS) or liquid-to-solid phase separation (LSPS) processes in biochemical analyses. Herein, we present common pitfalls of this assay caused by exceeding the detection linear range. We showed that aggregated proteins of high concentration and large particle size can lead to inaccurate quantification in multiple applications, including the optical density measurement, the thermal shift assay, and the dynamic light scattering experiment. Finally, we demonstrated that a simple sample dilution of insoluble aggregated protein (LSPS) samples or direct imaging of liquid droplets (LLPS) can address these issues and improve the accuracy of the turbidity assay.

Carboxy-Terminal Cementum Protein 1-Derived Peptide 4 (cemp1-p4) Promotes Mineralization through wnt/β-catenin Signaling in Human Oral Mucosa Stem Cells

Human cementum protein 1 (CEMP1) is known to induce cementoblast and osteoblast differentiation and alkaline phosphatase (ALP) activity in human periodontal ligament-derived cells in vitro and promotes bone regeneration in vivo. CEMP1's secondary structure analysis shows that it has a random-coiled structure and is considered an Intrinsic Disordered Protein (IDP). CEMP1's short peptide sequences mimic the biological capabilities of CEMP1. However, the role and mechanisms of CEMP1's C-terminal-derived synthetic peptide (CEMP1-p4) in the canonical Wnt/β-catenin signaling pathway are yet to be described. Here we report that CEMP1-p4 promotes proliferation and differentiation of Human Oral Mucosa Stem Cells (HOMSCs) by activating the Wnt/β-catenin pathway. CEMP1-p4 stimulation upregulated the expression of β-catenin and glycogen synthase kinase 3 beta (GSK-3B) and activated the transcription factors TCF1/7 and Lymphoid Enhancer binding Factor 1 (LEF1) at the mRNA and protein levels. We found translocation of β-catenin to the nucleus in CEMP1-p4-treated cultures. The peptide also penetrates the cell membrane and aggregates around the cell nucleus. Analysis of CEMP1-p4 secondary structure revealed that it has a random-coiled structure. Its biological activities included the induction to nucleate hydroxyapatite crystals. In CEMP1-p4-treated HOMSCs, ALP activity and calcium deposits increased. Expression of Osterix (OSX), Runt-related transcription factor 2 (RUNX2), Integrin binding sialoproptein (IBSP) and osteocalcin (OCN) were upregulated. Altogether, these data show that CEMP1-p4 plays a direct role in the differentiation of HOMSCs to a "mineralizing-like" phenotype by activating the β-catenin signaling cascade.

Human recombinant cementum attachment protein (hrPTPLa/CAP) promotes hydroxyapatite crystal formation in vitro and bone healing in vivo

Cementum extracellular matrix is similar to other mineralized tissues; however, this unique tissue contains molecules only present in cementum. A cDNA of these molecules, cementum attachment protein (hrPTPLa/CAP) was cloned and expressed in a prokaryotic system. This molecule is an alternative splicing of protein tyrosine phosphatase-like A (PTPLa). In this study, we wanted to determine the structural and functional characteristics of this protein. Our results indicate that hrPTPLa/CAP contains a 43.2% α-helix, 8.9% β-sheet, 2% β-turn and 45.9% random coil secondary structure. Dynamic light scattering shows that this molecule has a size distribution of 4.8 nm and aggregates as an estimated mass of 137 kDa species. AFM characterization and FE-SEM studies indicate that this protein self-assembles into nanospheres with sizes ranging from 7.0 to 27 nm in diameter. Functional studies demonstrate that hrPTPLa/CAP promotes hydroxyapatite crystal nucleation: EDS analysis revealed that hrPTPLa/CAP-induced crystals had a 1.59 ± 0.06 Ca/P ratio. Further confirmation with MicroRaman spectrometry and TEM confirm the presence of hydroxyapatite. In vivo studies using critical-size defects in rat cranium showed that hrPTPLa/CAP promoted 73% ± 2.19% and 87% ± 1.97% new bone formation at 4 and 8 weeks respectively. Although originally identified in cementum, PTPLa/CAP is very effective at inducing bone repair and healing and therefore this novel molecule has a great potential to be used for mineralized tissue bioengineering and tissue regeneration.

Biophysical characterization of recombinant proteins: a key to higher structural genomics success

Hundreds of genomes have been successfully sequenced to date, and the data are publicly available. At the same time, the advances in large-scale expression and purification of recombinant proteins have paved the way for structural genomics efforts. Frequently, however, little is known about newly expressed proteins calling for large-scale protein characterization to better understand their biochemical roles and to enable structure-function relationship studies. In the Structural Genomics Consortium (SGC), we have established a platform to characterize large numbers of purified proteins. This includes screening for ligands, enzyme assays, peptide arrays and peptide displacement in a 384-well format. In this review, we describe this platform in more detail and report on how our approach significantly increases the success rate for structure determination. Coupled with high-resolution X-ray crystallography and structure-guided methods, this platform can also be used toward the development of chemical probes through screening families of proteins against a variety of chemical series and focused chemical libraries.

Constructing ordered sensitized heterojunctions: bottom-up electrochemical synthesis of p-type semiconductors in oriented n-TiO(2) nanotube arrays

Fabrication of efficient semiconductor-sensitized bulk heterojunction solar cells requires the complete filling of the pore system of one semiconductor (host) material with nanoscale dimensions (<100 nm) with a different semiconductor (guest) material. Because of the small pore size and electrical conductivity of the host material, it is challenging to employ electrochemical approaches to fill the entire pore network. Typically, during the electrochemical deposition process, the guest material blocks the pores of the host, precluding complete pore filling. We describe a general synthetic strategy for spatially controlling the growth of p-type semiconductors in the nanopores of electrically conducting n-type materials. As an illustration of this strategy, we report on the facile electrochemical deposition of p-CuInSe(2) in nanoporous anatase n-TiO(2) oriented nanotube arrays and nanoparticle films. We show that by controlling the ambipolar diffusion length the p-type semiconductors can be deposited from the bottom-up, resulting in complete pore filling.

Lipid dependant disorder-to-order conformational transitions in apolipoprotein CI derived peptides

In contrast to the notion established for many years that protein function depends on rigid 3D structures, nowadays there is important evidence suggesting that non-structured segments of proteins play important roles in protein function. Therefore, disorder-to-order dynamic conformational transitions have been proposed as an attractive mechanism involved in protein-protein recognition. Our laboratory using Langmuir monolayers of apolipoproteins has previously shown that upon lateral compression at the air/water and phospholipid/water interfaces, there is an important movement of the C-terminal segment of apolipoprotein CI towards the air, considered the hydrophobic region of the monolayer and the acyl-chain region of the interface when phospholipids are used. Here, in an attempt to define secondary structure changes that might occur within this C-terminal segment of apoCI while moving from the monolayer interface back and forth its hydrophobic region, employing three peptides derived from apoCI we studied by circular dichroism and dynamic light scattering their conformational properties when associated to a series of amphipathic lipids and lipid-like molecules. Our results show that a series of lysophospholipids present the ability to modulate the formation of an alpha helix at the C-terminal peptide of apoCI through a disorder-to-order transition while forming small lipid/peptide aggregates below 10nm in diameter.

Recent developments in structural proteomics for protein structure determination

The major challenges in structural proteomics include identifying all the proteins on the genome-wide scale, determining their structure-function relationships, and outlining the precise three-dimensional structures of the proteins. Protein structures are typically determined by experimental approaches such as X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy. However, the knowledge of three-dimensional space by these techniques is still limited. Thus, computational methods such as comparative and de novo approaches and molecular dynamic simulations are intensively used as alternative tools to predict the three-dimensional structures and dynamic behavior of proteins. This review summarizes recent developments in structural proteomics for protein structure determination; including instrumental methods such as X-ray crystallography and NMR spectroscopy, and computational methods such as comparative and de novo structure prediction and molecular dynamics simulations.

High-throughput structural proteomics using x-rays

Following the recent sequencing of the human genome, the focus has shifted from the DNA level to the protein level, with the goal of elucidating function. Technical developments in x-ray crystallography mean that the crystal structures of these new proteins can now been determined at an unprecedented rate, which assists in functional analysis and rational drug-design programmes.