Free-energy landscapes of membrane co-translocational protein unfolding

Large and Stable Nanopores Formed by Complement Component 9 for Characterizing Single Folded Proteins

Biological nanopores offer a promising approach for single-molecule analysis of nucleic acids, peptides, and proteins. The work presented here introduces a biological nanopore formed by the self-assembly of complement component 9 (C9). This exceptionally large and cylindrical protein pore is composed of 20 ± 4 monomers of C9 resulting in a diameter of 10 ± 4 nm and an effective pore length of 13 nm. These poly(C9) pores remain stable for up to 30 min without indications of gating, flickering, or clogging across a range of transmembrane voltages (-150 to +150 mV) and ionic strengths (50 to 1000 mM). At physiologic pH, the ring-shaped distribution of negative and positive surface charges in the lumen of the pore enables capture of analyte proteins by electro-osmotic flow and leads to residence times of analyte proteins whose most probable values can exceed 300 μs. We used poly(C9) nanopores to determine the volume and shape of unlabeled folded proteins with molecular weights between 9 and 230 kDa with unprecedented accuracy in the context of resistive pulse recordings. Finally, poly(C9) pores made it possible to distinguish between the open and closed conformations of adenylate kinase based on differences in current modulations within resistive pulses and the corresponding differences in approximations of their shape. Thus, poly(C9) nanopores enable highly sensitive and accurate characterization of a wide range of natively folded proteins on a single molecule level.

Nanopore DNA sequencing technologies and their applications towards single-molecule proteomics

Sequencing of nucleic acids with nanopores has emerged as a powerful tool offering rapid readout, high accuracy, low cost and portability. This label-free method for sequencing at the single-molecule level is an achievement on its own. However, nanopores also show promise for the technologically even more challenging sequencing of polypeptides, something that could considerably benefit biological discovery, clinical diagnostics and homeland security, as current techniques lack portability and speed. Here we survey the biochemical innovations underpinning commercial and academic nanopore DNA/RNA sequencing techniques, and explore how these advances can fuel developments in future protein sequencing with nanopores.

Unidirectional single-file transport of full-length proteins through a nanopore

The electrical current blockade of a peptide or protein threading through a nanopore can be used as a fingerprint of the molecule in biosensor applications. However, threading of full-length proteins has only been achieved using enzymatic unfolding and translocation. Here we describe an enzyme-free approach for unidirectional, slow transport of full-length proteins through nanopores. We show that the combination of a chemically resistant biological nanopore, α-hemolysin (narrowest part is ~1.4 nm in diameter), and a high concentration guanidinium chloride buffer enables unidirectional, single-file protein transport propelled by an electroosmotic effect. We show that the mean protein translocation velocity depends linearly on the applied voltage and translocation times depend linearly on length, resembling the translocation dynamics of ssDNA. Using a supervised machine-learning classifier, we demonstrate that single-translocation events contain sufficient information to distinguish their threading orientation and identity with accuracies larger than 90%. Capture rates of protein are increased substantially when either a genetically encoded charged peptide tail or a DNA tag is added to a protein.

Herding cats: Label-based approaches in protein translocation through nanopore sensors for single-molecule protein sequence analysis

Proteins carry out life's essential functions. Comprehensive proteome analysis technologies are thus required for a full understanding of the operating principles of biological systems. While current proteomics techniques suffer from limitations in sensitivity and/or throughput, nanopore technology has the potential to enable de novo protein identification through single-molecule sequencing. However, a significant barrier to achieving this goal is controlling protein/peptide translocation through the nanopore sensor for processive strand analysis. Here, we review recent approaches that use a range of techniques, from oligonucleotide conjugation to molecular motors, aimed at driving protein strands and peptides through protein nanopores. We further discuss site-specific protein conjugation chemistry that could be combined with these translocation approaches as future directions to achieve single-molecule protein detection and sequencing of native proteins.

The emerging landscape of single-molecule protein sequencing technologies

Single-cell profiling methods have had a profound impact on the understanding of cellular heterogeneity. While genomes and transcriptomes can be explored at the single-cell level, single-cell profiling of proteomes is not yet established. Here we describe new single-molecule protein sequencing and identification technologies alongside innovations in mass spectrometry that will eventually enable broad sequence coverage in single-cell profiling. These technologies will in turn facilitate biological discovery and open new avenues for ultrasensitive disease diagnostics.

Single-aminoacid discrimination in proteins with homogeneous nanopore sensors and neural networks

A technology capable of sequencing individual protein molecules would revolutionize our understanding of biological processes. Nanopore technology can analyze single heteropolymer molecules such as DNA by measuring the ionic current flowing through a single nanometer hole made in an electrically insulating membrane. This current is sensitive to the monomer sequence. However, proteins are remarkably complex and identifying a single residue change in a protein remains a challenge. In this work, I show that simple neural networks can be trained to recognize protein mutants. Although these networks are quickly and efficiently trained, their ability to generalize in an independent experiment is poor. Using a thermal annealing protocol on the nanopore sample, and examining many mutants with the same nanopore sensor are measures aimed at reducing training data variability which produce an increase in the generalizability of the trained neural network. Using this approach, we obtain a 100% correct assignment among 9 mutants in >50% of the experiments. Interestingly, the neural network performance, compared to a random guess, improves as more mutants are included in the dataset for discrimination. Engineered nanopores prepared with high homogeneity coupled with state-of-the-art analysis of the ionic current signals may enable single-molecule protein sequencing.

Use of pore-forming toxins to study co-translocational protein folding

In vivo proteins fold mainly as they emerge from the ribosome or as they emerge from a membrane translocon. Membrane translocation in particular poses technical challenges to the study of the associated protein folding processes. Recently we have developed a single-molecule methodology that allows the capture of a single protein molecule through a membrane translocon with biotinylated oligonucleotides covalently bound at its N- and C- terminus using streptavidin. The resulting rotaxane can be driven forwards and backwards changing the voltage polarity, and carefully planned experiments allow inference of the folding pathway. Here we will discuss the details of a simplified methodological approach.

Biological Nanopores: Engineering on Demand

Nanopore-based sensing is a powerful technique for the detection of diverse organic and inorganic molecules, long-read sequencing of nucleic acids, and single-molecule analyses of enzymatic reactions. Selected from natural sources, protein-based nanopores enable rapid, label-free detection of analytes. Furthermore, these proteins are easy to produce, form pores with defined sizes, and can be easily manipulated with standard molecular biology techniques. The range of possible analytes can be extended by using externally added adapter molecules. Here, we provide an overview of current nanopore applications with a focus on engineering strategies and solutions.