A theoretical justification for single molecule peptide sequencing

Highly parallel single-molecule identification of proteins in zeptomole-scale mixtures

The identification and quantification of proteins lags behind DNA-sequencing methods in scale, sensitivity, and dynamic range. Here, we show that sparse amino acid-sequence information can be obtained for individual protein molecules for thousands to millions of molecules in parallel. We demonstrate selective fluorescence labeling of cysteine and lysine residues in peptide samples, immobilization of labeled peptides on a glass surface, and imaging by total internal reflection microscopy to monitor decreases in each molecule's fluorescence after consecutive rounds of Edman degradation. The obtained sparse fluorescent sequence of each molecule was then assigned to its parent protein in a reference database. We tested the method on synthetic and naturally derived peptide molecules in zeptomole-scale quantities. We also fluorescently labeled phosphoserines and achieved single-molecule positional readout of the phosphorylated sites. We measured >93% efficiencies for dye labeling, survival, and cleavage; further improvements should enable studies of increasingly complex proteomic mixtures, with the high sensitivity and digital quantification offered by single-molecule sequencing.

Paving the way to single-molecule protein sequencing

Proteins are major building blocks of life. The protein content of a cell and an organism provides key information for the understanding of biological processes and disease. Despite the importance of protein analysis, only a handful of techniques are available to determine protein sequences, and these methods face limitations, for example, requiring a sizable amount of sample. Single-molecule techniques would revolutionize proteomics research, providing ultimate sensitivity for the detection of low-abundance proteins and the realization of single-cell proteomics. In recent years, novel single-molecule protein sequencing schemes that use fluorescence, tunnelling currents and nanopores have been proposed. Here, we present a review of these approaches, together with the first experimental efforts towards their realization. We discuss their advantages and drawbacks, and present our perspective on the development of single-molecule protein sequencing techniques.

Single-molecule peptide fingerprinting

Proteomic analyses provide essential information on molecular pathways of cellular systems and the state of a living organism. Mass spectrometry is currently the first choice for proteomic analysis. However, the requirement for a large amount of sample renders a small-scale proteomics study challenging. Here, we demonstrate a proof of concept of single-molecule FRET-based protein fingerprinting. We harnessed the AAA+ protease ClpXP to scan peptides. By using donor fluorophore-labeled ClpP, we sequentially read out FRET signals from acceptor-labeled amino acids of peptides. The repurposed ClpXP exhibits unidirectional processing with high processivity and has the potential to detect low-abundance proteins. Our technique is a promising approach for sequencing protein substrates using a small amount of sample.

Single-molecule protein identification by sub-nanopore sensors

Recent advances in top-down mass spectrometry enabled identification of intact proteins, but this technology still faces challenges. For example, top-down mass spectrometry suffers from a lack of sensitivity since the ion counts for a single fragmentation event are often low. In contrast, nanopore technology is exquisitely sensitive to single intact molecules, but it has only been successfully applied to DNA sequencing, so far. Here, we explore the potential of sub-nanopores for single-molecule protein identification (SMPI) and describe an algorithm for identification of the electrical current blockade signal (nanospectrum) resulting from the translocation of a denaturated, linearly charged protein through a sub-nanopore. The analysis of identification p-values suggests that the current technology is already sufficient for matching nanospectra against small protein databases, e.g., protein identification in bacterial proteomes.

Protein identification is the key step in many proteomics studies. Currently, the most popular technique for intact protein analysis is top-down mass spectrometry which recently enabled high-throughput identification of many proteins and their proteoforms. However, this approach requires large amounts of materials and is currently limited to short proteins, typically less than 30 kDa. On the other hand, nanopore sensors promise single molecule sensitivity in protein analysis, but an approach for the identification of a single protein from its blockade current (nanospectrum) has remained elusive, since the signal from the sensors relates to the amino acid sequence of the protein in a poorly understood way. In this work we describe the first algorithm for protein identification based on nanospectra associated with translocation of proteins through pores with sub-nanometer diameters. While identification accuracy currently does not allow reliable processing of complex protein samples yet, we believe, that the rapidly improving experimental protocols along with the new computational algorithms will transform into a viable protein identification approach in the near future.

Solution-phase and solid-phase sequential, selective modification of side chains in KDYWEC and KDYWE as models for usage in single-molecule protein sequencing

Single-molecule protein sequencing is regarded as a promising new method in the field of proteomics. It potentially offers orders of magnitude improvements in sensitivitiy and throughput for protein detection when compared to mass spectrometry. However, the development of such a technology faces significant barriers, especially in the need to chemically derivatize specific amino-acid types with unique labels. For example, fluorescent dyes would be suitable for single-molecule microscopy or nanopore-based sequencing. These emerging single-molecule protein-sequencing technologies suggests a need to develop an amino acid side chain-selective modification scheme that could target several side chains of interest. Current work for modifying residues focuses mainly on one or two side chains. The need to label many side chains, as recent computational modeling suggests, is required for high protein, sequencing coverage of the human proteome. Herein, we report our stragety for modifying two model peptides KYDWEC and KDYWE containing the most reactive residues, using highly opitmized mass labels in a sequential and selective fashion both using solution-phase and solid-phase chemistries, respectively. This will serve as a step towards a modification scheme appropriate for single-molecule studies.

Single-molecule protein sequencing through fingerprinting: computational assessment

Proteins are vital in all biological systems as they constitute the main structural and functional components of cells. Recent advances in mass spectrometry have brought the promise of complete proteomics by helping draft the human proteome. Yet, this commonly used protein sequencing technique has fundamental limitations in sensitivity. Here we propose a method for single-molecule (SM) protein sequencing. A major challenge lies in the fact that proteins are composed of 20 different amino acids, which demands 20 molecular reporters. We computationally demonstrate that it suffices to measure only two types of amino acids to identify proteins and suggest an experimental scheme using SM fluorescence. When achieved, this highly sensitive approach will result in a paradigm shift in proteomics, with major impact in the biological and medical sciences.