Preparation of Recombinant Membrane Proteins from Pichia pastoris for Molecular Investigations

Development of ultra-miniaturized weak affinity chromatography coupled to mass spectrometry as a high throughput fragment screening method against wild-type and purified membrane proteins embedded in biomimetic membranes

BACKGROUND

Membrane proteins, which make up approximately 30 % of the proteome, are important drug targets but present many challenges in drug discovery, including limited production rates, low final yields of pure and functionally folded proteins, and instability in aqueous media. The problems encountered with membrane proteins are even more critical in the Fragment Based Drug Discovery, where the discovery of potential drug candidates is hampered by the limited availability of efficient methods for rapid screening of weak fragment-protein interactions.

RESULTS

In this work, we propose the coupling of miniaturized weak affinity chromatography with mass spectrometry (nano-WAC-MS) as an innovative strategy for the rapid screening of fragments capable of weak binding to a selected membrane protein. An integral membrane protein (AA2AR) was incorporated into biotinylated nanodiscs, which were subsequently immobilized on a miniaturized monolithic streptavidin column (75 μm i.d., 300 nL volume). The coupling of these miniaturized affinity columns (each consuming less than 1 μg of protein) to mass spectrometry (MRM mode) has been optimized to maximize the low affinity range and increase throughput so that 150 fragments can be injected in a single analysis, with a DMSO content as high as 10 %, with no influence on the affinity. Hits are identified by comparing their retention with that measured on control columns prepared with empty nanodiscs.

SIGNIFICANCE

The results of this screening are compared with those obtained by NMR and newly identified hits are confirmed by either competition experiments or frontal affinity experiments. We show that this nanodisc-based strategy, which provides a stable and native-like lipid environment for the protein (columns can be used for several days), should also work with other membrane proteins embedded in nanodiscs.

Ligand Screening of Membrane Proteins Embedded in Nanodiscs: How to Manage Non-Specific Interactions in Weak Affinity Chromatography?

Miniaturized weak affinity chromatography is emerging as an interesting alternative to conventional biophysical tools for performing fragment-screening studies in the context of fragment-based drug discovery. In order to push back the analytical limits, it is necessary not only to control non-specific interactions with chromatographic support, but also to adapt this methodology by comparing the results obtained on an affinity column to a control column. The work presented in this study focused on fragment screening that targets a model membrane protein, the adenosine A2A receptor, embedded in nanodiscs (NDs) as biomimetic membranes. By studying the retention behavior of test fragment mixtures on supports modified with different types of NDs, we were able to determine the contribution of ND-related non-specific interactions, in particular the electrostatic effect of anionic phospholipids and the hydrophobic effect of neutral phospholipids. Different strategies for the preparation of control columns (empty NDs, orthosteric site blocking) were investigated and are presented for the first time. With these two types of control columns, the screening enabled the identification of two new fragments of AA2AR, which were confirmed by competition experiments and whose Kd values, estimated directly during the screening or after the competition experiments in frontal mode, were in good agreement.

Cloning and Overexpressing Membrane Proteins Using Pichia pastoris (Komagataella phaffii)

Understanding the structure and function of key proteins located within biological membranes is essential for fundamental knowledge and therapeutic applications. Robust cell systems allowing their actual overexpression are required, among which stands the methylotrophic yeast Pichia pastoris. This system proves highly efficient in producing many eukaryotic membrane proteins of various functions and structures at levels and quality compatible with their subsequent isolation and molecular investigation. This article describes a set of basic guidelines and directions to clone and select recombinant P. pastoris clones overexpressing eukaryotic membrane proteins. Illustrative results obtained for a panel of mammalian membrane proteins are presented, and hints are given on a series of experimental parameters that may substantially improve the amount and/or the functionality of the expressed proteins. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Designing and cloning a P. pastoris expression vector Basic Protocol 2: Integrative transformation of P. pastoris and selection of recombinant clones Basic Protocol 3: Culturing transformed P. pastoris for membrane protein expression Basic Protocol 4: Yeast cell lysis and membrane preparation Basic Protocol 5: Immunodetection of expressed membrane proteins: western blot Alternate Protocol 1: Immunodetection of expressed membrane proteins: dot blot Alternate Protocol 2: Immunodetection of expressed membrane proteins: yeastern blot Basic Protocol 6: Activity assay: ligand-binding analysis of an expressed GPCR.

Plant cellulose synthase membrane protein isolation directly from Pichia pastoris protoplasts, liposome reconstitution, and its enzymatic characterization

Cellulose is synthesized by a plant cell membrane-integrated processive glycosyltransferase (GT) called cellulose synthase (CesA). Since only a few of these plant CesAs have been purified and characterized to date, there are huge gaps in our mechanistic understanding of these enzymes. The biochemistry and structural biology studies of CesAs are currently hampered by challenges associated with their expression and extraction at high yields. To aid in understanding CesA reaction mechanisms and to provide a more efficient CesA extraction method, two putative plant CesAs - PpCesA5 from Physcomitrella patens and PttCesA8 from Populus tremula x tremuloides that are involved in primary and secondary cell wall formation in plants were expressed using Pichia pastoris as an expression host. We developed a protoplast-based membrane protein extraction approach to directly isolate these membrane-bound enzymes, as confirmed by immunoblotting and mass spectrometry-based analyses. Our method gives 3-4-fold higher purified protein yield than the standard cell homogenization protocol. Our method resulted in liposome reconstituted CesA5 and CesA8 enzymes with similar Michaelis-Menten kinetic constants, K_m = 167 μM, 108 μM and V_max = 7.88 × 10^-5 μmol/min, 4.31 × 10^-5 μmol/min, respectively, in concurrence with the previous studies for enzymes isolated using the standard protocol. Taken together, these results suggest that CesAs involved in primary and secondary cell wall formation can be expressed and purified using a simple and more efficient extraction method. This protocol could help isolate enzymes that unravel the mechanism of native and engineered cellulose synthase complexes involved in plant cell wall biosynthesis.

Mini-Bioreactor Platform for Membrane Protein Production in Komagataella pastoris

Membrane proteins (MPs) play vital roles across various cellular functions, biological processes, physiological signaling pathways, and human-related disorders. Considering the clinical relevance of MPs and their application as therapeutic targets, it is crucial to explore highly effective production platforms and purification approaches to ultimately obtain a high-resolution structure of the target. Therefore, it would be possible to gather detailed knowledge on their mechanism of action which will be the basis for the rational design of novel and stronger drugs. Unfortunately, when compared to their soluble counterparts, 3D structures of MPs are really scarce (<2%), mainly due to poorly natural abundance, challenges associated with protein solubility and stability, and difficulties in producing bioactive and properly structural folded targets. These drawbacks could significantly impair the use of MPs as therapeutic targeting and demand efforts to develop tailor-made strategies for their appropriate handling. Therefore, this chapter is focused on describing a detailed and high-throughput procedure for the biosynthesis of MPs using Komagataella pastoris cell cultures as expression system in a mini-bioreactor platform. Additionally, insights on a purification strategy that combines immobilized-metal affinity and ion-exchange chromatography are described to further obtain the target protein with a significant degree of purity.

Heterologous (Over) Expression of Human SoLute Carrier (SLC) in Yeast: A Well-Recognized Tool for Human Transporter Function/Structure Studies

For more than 20 years, yeast has been a widely used system for the expression of human membrane transporters. Among them, more than 400 are members of the largest transporter family, the SLC superfamily. SLCs play critical roles in maintaining cellular homeostasis by transporting nutrients, ions, and waste products. Based on their involvement in drug absorption and in several human diseases, they are considered emerging therapeutic targets. Despite their critical role in human health, a large part of SLCs' is 'orphans' for substrate specificity or function. Moreover, very few data are available concerning their 3D structure. On the basis of the human health benefits of filling these knowledge gaps, an understanding of protein expression in systems that allow functional production of these proteins is essential. Among the 500 known yeast species, S. cerevisiae and P. pastoris represent those most employed for this purpose. This review aims to provide a comprehensive state-of-the-art on the attempts of human SLC expression performed by exploiting yeast. The collected data will hopefully be useful for guiding new attempts in SLCs expression with the aim to reveal new fundamental data that could lead to potential effects on human health.

MT1 Melatonin Receptor Reconstitution in Nanodiscs

A way to study G protein-coupled receptors in a minimal system is to reconstruct artificial membrane mimics, made of detergent and/or of lipids in which the purified receptor is maintained. In particular, it is now possible to generate lipid nanoparticles, such as nanodiscs, in which a single receptor molecule is included. Such objects offer the invaluable potential of studying an isolated receptor stabilized in a finely controlled membrane-like environment to evaluate its pharmacology, its function, and its structure at the molecular level. In this chapter, we detail the different steps from the extraction and isolation of a recombinant MT1 melatonin receptor in detergent, down to its reconstitution into nanodiscs. A G protein activation test is further described in order to exemplify how the functionality of such particles may be investigated.

Production and Preparation of Isotopically Labeled Human Membrane Proteins in Pichia pastoris for Fast-MAS-NMR Analyses

Membrane proteins (MPs) comprise about one-third of the human proteome, playing critical roles in many physiological processes and associated disorders. Consistently, they represent one of the largest classes of targets for the pharmaceutical industry. Their study at the molecular level is however particularly challenging, resulting in a severe lack of structural and dynamic information that is hindering their detailed functional characterization and the identification of novel potent drug candidates.Magic Angle Spinning (MAS) NMR is a reliable and efficient method for the determination of protein structures and dynamics and for the identification of ligand binding sites and equilibria. MAS-NMR is particularly well suited for MPs since they can be directly analysed in a native-like lipid bilayer environment but used to require aggravating large amounts of isotope enriched material. The frequent toxicity of human MP overexpression in bacterial cultures poses an additional hurdle, resulting in the need for alternative (and often more costly) expression systems. The recent development of very fast (up to 150 kHz) MAS probes has revolutionized the field of biomolecular solid-state NMR enabling higher spectral resolution with significant reduction of the required sample, rendering eukaryotic expression systems cost-effective.Here is presented a set of accessible procedures validated for the production and preparation of eukaryotic MPs for Fast-MAS ¹H-detected NMR analysis. The methodology is illustrated with the human copper uptake protein hCTR1 recombinantly produced and ¹³C-¹⁵N uniformly labeled with the versatile and affordable Pichia pastoris system. Subsequent purification procedures allow the recovery of mg amounts that are then reconstituted into liposome formulations compatible with solid-state NMR handling and analysis.

Therapeutic Antibodies Targeting Potassium Ion Channels

Monoclonal antibodies combine specificity and high affinity binding with excellent pharmacokinetic properties and are rapidly being developed for a wide range of drug targets including clinically important potassium ion channels. Nonetheless, while therapeutic antibodies come with great promise, K⁺ channels represent particularly difficult targets for biologics development for a variety of reasons that include their dynamic structures and relatively small extracellular loops, their high degree of sequence conservation (leading to immune tolerance), and their generally low-level expression in vivo. The process is made all the more difficult when large numbers of antibody candidates must be screened for a given target, or when lead candidates fail to cross-react with orthologous channels in animal disease models due to their highly selective binding properties. While the number of antibodies targeting potassium channels in preclinical or clinical development is still modest, significant advances in the areas of protein expression and antibody screening are converging to open the field to an avalanche of new drugs. Here, the opportunities and constraints associated with the discovery of antibodies against K⁺ channels are discussed, with an emphasis on novel technologies that are opening the field to exciting new possibilities for biologics development.