Structural basis for cooperative oxygen binding and bracelet-assisted assembly of Lumbricus terrestris hemoglobin

Isolation, identification of antioxidant peptides from earthworm proteins and analysis of the structure-activity relationship of the peptides based on quantum chemical calculations

Earthworms are emerging sources of edible animal proteins. Earthworm extracts exhibit good in vivo antioxidant activity after oral administration. To better understand the antioxidant activity of earthworms, antioxidant peptides derived from earthworm proteins after gastrointestinal digestion were isolated and identified, and their structure-activity relationships were analysed in this research. Results showed that earthworm protein gastrointestinal digestion products exhibited good antioxidant activity, and 6030 peptide sequences were identified after separation using ion-exchange and gel-chromatography columns. Eleven peptides were screened using computer simulation activity scores, among which AFWYGLPCKL, WPWQMSLY, and GCFRYACGAFY showed the best antioxidant activities. Highest Occupied Molecular Orbital (HOMO) analysis indicated that N29-H10, O122-H38, and the peptide bond binding sites of serine and leucine were active sites of peptides AFWYGLPCKL, GCFRYACGAFY, and WPWQMSLY, respectively. This study provides a new understanding of substance basis of antioxidant activity in earthworms and contributes to application of earthworm proteins as antioxidants in health-foods.

Identification of genomic loci regulating grain iron content in aus rice under two irrigation management systems

Iron (Fe) deficiency is one of the common causes of anaemia in humans. Improving grain Fe in rice, therefore, could have a positive impact for humans worldwide, especially for those people who consume rice as a staple food. In this study, 225–269 accessions of the Bengal and Assam Aus Panel (BAAP) were investigated for their accumulation of grain Fe in two consecutive years in a field experiment under alternative wetting and drying (AWD) and continuous flooded (CF) irrigation. AWD reduced straw Fe by 40% and grain Fe by 5.5–13%. Genotype differences accounted for 35% of the variation in grain Fe, while genotype by irrigation interaction accounted for 12% of the variation in straw and grain Fe in year 1, with no significant interactions detected in year 2. Twelve rice accessions were identified as having high grain Fe for both years regardless of irrigation treatment, half of which were from BAAP aus subgroup 3 which prominently comes from Bangladesh. On average, subgroup 3 had higher grain Fe than the other four subgroups of aus. Genome‐wide association mapping identified 6 genomic loci controlling natural variation of grain Fe concentration in plants grown under AWD. For one QTL, nicotianamine synthase OsNAS3 is proposed as candidate for controlling natural variation of grain Fe in rice. The BAAP contains three haplotypes of OsNAS3 where one haplotype (detected in 31% of the individuals) increased grain Fe up to 11%. Haplotype analysis of this gene in rice suggests that the ability to detect the QTL is enhanced in the BAAP because the high Fe allele is balanced in aus, unlike indica and japonica subgroups.

Insight to Functional Conformation and Noncovalent Interactions of Protein-Protein Assembly Using MALDI Mass Spectrometry

Noncovalent interactions are the keys to the structural organization of biomolecule e.g., proteins, glycans, lipids in the process of molecular recognition processes e.g., enzyme-substrate, antigen-antibody. Protein interactions lead to conformational changes, which dictate the functionality of that protein-protein complex. Besides biophysics techniques, noncovalent interaction and conformational dynamics, can be studied via mass spectrometry (MS), which represents a powerful tool, due to its low sample consumption, high sensitivity, and label-free sample. In this review, the focus will be placed on Matrix-Assisted Laser Desorption Ionization Mass Spectrometry (MALDI-MS) and its role in the analysis of protein-protein noncovalent assemblies exploring the relationship within noncovalent interaction, conformation, and biological function.

Purification of Lumbricus terrestris Mega-Hemoglobin for Diverse Oxygen Therapeutic Applications

Oxygen therapeutics are being developed for a variety of applications in transfusion medicine. In order to reduce the side-effects (vasoconstriction, systemic hypertension, and oxidative tissue injury) associated with previous generations of oxygen therapeutics, new strategies are focused on increasing the molecular diameter of hemoglobin obtained from mammalian sources via polymerization and encapsulation. Another approach towards oxygen therapeutic design has centered on using naturally occurring large molecular diameter hemoglobins (i.e. erythrocruorins) derived from annelid sources. Therefore, the goal of this study was to purify erythrocruorin from the terrestrial worm Lumbricus terrestris for diverse oxygen therapeutic applications. Tangential flow filtration (TFF) was used as a scalable protein purification platform to obtain a >99% pure LtEc product, which was confirmed by size exclusion high performance liquid chromatography and SDS-PAGE analysis. In vitro characterization concluded that the ultra-pure LtEc product had oxygen equilibrium properties similar to human red blood cells, and a lower rate of auto-oxidation compared to human hemoglobin, both of which should enable efficient oxygen transport under physiological conditions. In vivo evaluation concluded that the ultra-pure product had positive effects on the microcirculation sustaining functional capillary density compared to a less pure product (~86% purity). In summary, we purified an LtEc product with favorable biophysical properties that performed well in an animal model using a reliable and scalable purification platform to eliminate undesirable proteins.

In Situ Analysis of Weakly Bound Proteins Reveals Molecular Basis of Soft Corona Formation

Few experimental techniques allow the analysis of the protein corona in situ. As a result, little is known on the effects of nanoparticles on weakly bound proteins that form the soft corona. Despite its biological importance, our understanding of the molecular bases driving its formation is limited. Here, we show that hemoglobin can form either a hard or a soft corona on silica nanoparticles depending on the pH conditions. Using cryoTEM and synchrotron-radiation circular dichroism, we show that nanoparticles alter the structure and the stability of weakly bound proteins in situ. Molecular dynamics simulation identified the structural elements driving protein-nanoparticle interaction. Based on thermodynamic analysis, we show that nanoparticles stabilize partially unfolded protein conformations by enthalpy-driven molecular interactions. We suggest that nanoparticles alter weakly bound proteins by shifting the equilibrium toward the unfolded states at physiological temperature. We show that the classical approach based on nanoparticle separation from the biological medium fails to detect destabilization of weakly bound proteins, and therefore cannot be used to fully predict the biological effects of nanomaterials in situ.

Low-energy in-line electron holographic imaging of vitreous ice-embedded small biomolecules using a modified scanning electron microscope

Cryo-electron microscopy (cryo-EM) has become the method of choice in the field of structural biology, owing to its unique ability to deduce structures of vitreous ice-embedded, hydrated biomolecules over a wide range of structural resolutions. As cryo-transmission electron microscopes (cryo-TEM) become increasingly specialised for high, near-atomic resolution studies, operational complexity and associated costs serve as significant barriers to widespread usability and adoptability. To facilitate the expansion and accessibility of the cryo-EM method, an efficient, user-friendly means of imaging vitreous ice-embedded biomolecules has been called for. In this study, we present a solution to this issue by integrating cryo-EM capabilities into a commercial scanning electron microscope (SEM). Utilising the principle of low-energy in-line electron holography, our newly developed hybrid microscope permits low-to-moderate resolution imaging of vitreous ice-embedded biomolecules without the need for any form of sample staining or chemical fixation. Operating at 20 kV, the microscope takes advantage of the ease-of-use of SEM-based imaging and phase contrast imaging of low-energy electron holography. This study represents the first reported successful application of low-energy in-line electron holographic imaging to vitreous ice-embedded small biomolecules, the effectiveness of which is demonstrated here with three morphologically distinct specimens.