Infinite re-reading of single proteins at single-amino-acid resolution using nanopore sequencing

As identifying proteins is of paramount importance for cell biology and applications, it is of interest to develop a protein sequencer with the ultimate sensitivity of decoding individual proteins. Here, we demonstrate a nanopore-based single-molecule sequencing approach capable of reliably detecting single amino-acid substitutions within individual peptides. A peptide is linked to a DNA molecule that is pulled through the biological nanopore MspA by a DNA helicase in single amino-acid steps. The peptide sequence yields clear stepping ion current signals which allows to discriminate single-amino-acid substitutions in single reads. Molecular dynamics simulations show these signals to result from size exclusion and pore binding. Notably, we demonstrate the capability to 'rewind' peptide reads, obtaining indefinitely many independent reads of the same individual molecule, yielding virtually 100% read accuracy in variant identification, with an error rate less than 10-6. These proof-of-concept experiments constitute a promising basis for developing a single-molecule protein sequencer.

Purification, Identification, Activity Evaluation, and Stability of Antioxidant Peptides from Alcalase Hydrolysate of Antarctic Krill (Euphausia superba) Proteins

For utilizing the largest source of marine proteins, Antarctic krill (Euphausia superba) proteins were defatted and hydrolyzed separately using pepsin, alcalase, papain, trypsin, and netrase, and alcalase hydrolysate (EPAH) showed the highest DPPH radical (DPPH·) and hydroxyl radical (HO·) scavenging activity among five hydrolysates. Using ultrafiltration and chromatography methods, fifteen antioxidant peptides were purified from EPAH and identified as Asn-Gln-Met (NQM), Trp-Phe-Pro-Met (WFPM), Gln-Asn-Pro-Thr (QNPT), Tyr-Met-Asn-Phe (YMNF), Ser-Gly-Pro-Ala (SGPA), Ser-Leu-Pro-Tyr (SLPY), Gln-Tyr-Pro-Pro-Met-Gln-Tyr (QYPPMQY), Glu-Tyr-Glu-Ala (EYEA), Asn-Trp-Asp-Asp-Met-Arg-Ile-Val-Ala-Val (NWDDMRIVAV), Trp-Asp-Asp-Met-Glu-Arg-Leu-Val-Met-Ile (WDDMERLVMI), Asn-Trp-Asp-Asp-Met-Glu-Pro-Ser-Phe (NWD-DMEPSF), Asn-Gly-Pro-Asp-Pro-Arg-Pro-Ser-Gln-Gln (NGPDPRPSQQ), Ala-Phe-Leu-Trp-Asn (AFLWA), Asn-Val-Pro-Asp-Met (NVPDM), and Thr-Phe-Pro-Ile-Tyr-Asp-Tyr-Pro-Gln (TFPIYDPQ), respectively, using a protein sequencer and ESI/MS. Among fifteen antioxidant peptides, SLPY, QYPPMQY and EYEA showed the highest scavenging activities on DPPH· (EC50 values of 1.18 ± 0.036, 1.547 ± 0.150, and 1.372 ± 0.274 mg/mL, respectively), HO· (EC50 values of 0.826 ± 0.027, 1.022 ± 0.058, and 0.946 ± 0.011 mg/mL, respectively), and superoxide anion radical (EC50 values of 0.789 ± 0.079, 0.913 ± 0.007, and 0.793 ± 0.056 mg/mL, respectively). Moreover, SLPY, QYPPMQY and EYEA showed strong reducing power, protective capability against H2O2-damaged plasmid DNA, and lipid peroxidation inhibition ability. Furthermore, SLPY, QYPPMQY, and EYEA had high stability under temperatures lower than 80 °C, pH values ranged from 6–8, and simulated GI digestion for 180 min. The results showed that fifteen antioxidant peptides from alcalase hydrolysate of Antarctic krill proteins, especially SLPY, QYPPMQY and EYEA, might serve as effective antioxidant agents applied in food and health products.

Identification and Active Evaluation of Antioxidant Peptides from Protein Hydrolysates of Skipjack Tuna (Katsuwonus pelamis) Head

For the full use of fish by-products to produce antioxidant peptides, skipjack tuna (Katsuwonus pelamis) heads generated during can processing were defatted and hydrolyzed using the in vitro gastrointestinal (GI) digestion (pepsin–trypsin system) method and six antioxidant peptides (P1 to P6) were purified from the head hydrolysate (KPH) using ultrafiltration and serial chromatography methods. Six isolated peptides (P1 to P6) were identified as Val-Glu-Glu (VEE, P1), Trp-Met-Phe-Asp-Trp (WMFDW, P2), Asp-Ala-Gly-Pro-Tyr-Gly-Pro-Ile (DAGPYGPI, P3), Trp-Met-Gly-Pro-Tyr (WMGPY, P4), Glu-Arg-Gly-Pro-Leu-Gly-Pro-His (ERGPLGPH, P5), and Glu-Met- Gly-Pro-Ala (EMGPA, P6), respectively, using a protein sequencer and electrospray ionization-mass spectrometer. Among skipjack tuna head hydrolysates, fractions, and six isolated peptides (P1 to P6), WMFDW (P2), WMGPY (P4), and EMGPA (P6) showed the highest radical scavenging activities on 2,2-diphenyl-1-picrylhydrazyl (DPPH) (EC50 values of 0.31, 0.33, and 0.46 mg/mL for WMFDW, WMGPY, and EMGPA, respectively), hydroxyl (EC50 values of 0.30, 0.43, and 0.52 mg/mL for WMFDW, WMGPY, and EMGPA, respectively), and superoxide anion (EC50 values of 0.56, 0.38, and 0.71 mg/mL for WMFDW, WMGPY, and EMGPA, respectively). Moreover, WMFDW, WMGPY, and EMGPA showed strong capability in reducing power and lipd peroxidation inhibition in the linoleic acid system. In addition, WMFDW, WMGPY, and EMGPA can retain strong antioxidant activity at temperatures lower than 60 °C and pH values ranged from 5 to 9. The results showed that six isolated peptides (P1 to P6) from skipjack tuna heads, especially WMFDW, WMGPY, and EMGPA, might be applied in health care products acting as powerful antioxidant agents.

Electronic transport in a graphene single layer: application in amino acid sensing

We modeled a type of field-effect transistor device based on graphene for the recognition of amino acids with a potential application in the building of a protein sequencer.

An Efficient Scheduling Technique for Biological Sequence Alignment

Computing alignment matrix score to search for regions of homology between biological sequences is time consuming task. This is due to the recursive nature of the dynamic programming-based algorithms such as the Smith-Waterman and the Needleman-Wunsch algorithmns. Typical FPGA-based protein sequencer comprises of two main logic blocks. One for computing alignment scores i.e. the processing element (PE), while another logic block for configuring the PE with coefficients. During alignment matrix computation, the logic block for configuring the PE are left unused until the time consuming alignment matrix computation finished. Therefore, a new technique, known as overlap computation and configuration (OCC) is proposed to minimize the time overhead for performing biological sequence alignment. The OCC technique simultaneously updating substitution matrix in a processing element (PE) systolic array, while computing alignment matrix scores. Results showed that, the sequencer achieves more than two order of magnitude speed-up higher compared to the state of the art, at negligible area overhead, if any.

Isolation and Identification of Antioxidant Peptides from Black Soybean Protein

The aim of this work was to isolate and identify antioxidant peptides from black soybean protein hydrolysates (BSH) by using the ultrafiltration (UF) and macroporous adsorption resin (MAR), and the fraction BSP-DA-c performed high antioxidant activity was further purified using consecutive methods on Sephadex G-25 column and reversed phase high-performance liquid chromatography (RH-HPLC). Two highly purified antioxidant peptides SBP3 and BSPb were got, and their amino acid sequences were confirmed as Trp-Asn-Pro and Tyr-Asn-Ile by automated Edman degradation with a protein sequencer, respectively.